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Introduction

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Introduction
Mimics interfaces between scanner data (CT, MRI, Technical scanner, ...) and Rapid Prototyping, STL file format, CAD and Finite Element analysis. The Mimics software is an image-processing package with 3D visualization functions that interfaces with all common scanner formats. Additional modules provide the interface towards Rapid Prototyping using STL or direct layer formats with support. Alternatively, an interface to CAD (design of custom made prosthesis and new product lines based on image data) or to Finite Element meshes is available. Materialise's Interactive Medical Image Control System (MIMICS) is an interactive tool for the visualization and segmentation of CT images as well as MRI images and 3D rendering of objects. Therefore, in the medical field Mimics can be used for diagnostic, operation planning or rehearsal purposes. A very flexible interface to rapid prototyping systems is included for building distinctive segmentation objects. The software enables the user to control and correct the segmentation of CT-scans and MRI-scans. For instance, image artifacts coming from metal implants can easily be removed. The object(s) to be visualized and/or produced can be defined exactly by medical staff. No technical knowledge is needed for creating on screen 3D visualizations of medical objects (a cranium, pelvis, etc.) Separate software is available to define and calculate the necessary data to build the medical object(s) created within Mimics on all rapid prototyping systems. Mimics is a general-purpose segmentation program for gray value images. It can process any number of 2D image slices (rectangular images are allowed). The only restriction is the physical memory of your computer. The interface created to process the images provides several segmentation and visualization tools.

Overview Mimics modules
Mimics consists of five modules. The image below shows the links between the main program and its modules.

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Mimics
Mimics interactively read CT/MRI data in the DICOM format. Segmentation and editing tools enable the user to manipulate the data to select bone, soft tissue, skin, etc. Once an area of interest is separated, it can be visualized in 3D. After this visualization, a file can be made to interface with STL+ or MedCAD. CAD data, imported as STL files, can be visualized in 2D and 3D for design validation based on the anatomical geometry.

Import Module
Import module imports CT and MRI data from a wide variety of scanner formats. The data can be accessed from CD, optical disk, DAT tapes, 4 mm tapes, etc.

RP Slice Module
RP Slice module provides an interface to Rapid Prototyping systems via sliced files with patented support structure generation. The perforated support structures are generated in no time and use less material. Supported formats:

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  

Common Layer Interface Files (*.cli) 3D Systems Layer Interface Files (*.sli) 3D Systems Contour Files (*.slc)

STL+ Module
STL+ module provides interface options via triangulated formats. Supported formats:     STL (ASCII and Binary) DXF VRML PLY

MedCAD Module
MedCAD module provides a direct interface to CAD systems via surfaces, curves, and objects exported as IGES files. Supported files:   B-Spline (NURB) curves and surfaces exported as IGES Point Cloud

Simulation Module
The Simulation module is an open platform for surgical simulations. You can perform a detailed analysis of your data using the anthropometric analysis, plan osteotomies and distraction surgeries or simulate and explain a surgical procedure for your implant design.

FEA Module
The FEA module provides an interfacing to FEA (Finite Element Analysis) and CFD (Computational Fluid Dynamics). Supported formats:      Patran Neutral Abaqus Ansys Fluent Nastran

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What's new
Basic Mimics module
Upgraded User Interface
With the well-organized, intuitive user interface, you can quickly access all relevant tools and functions. Changes to the user interface include a redesign of the graphical elements to conform to “Windows XP” style, as well as a clearer organization of related functions and options.

Adjust Grayscale
The Adjust Gray Scale toolbar is replaced with a Contrast Histogram. This histogram allows you to do windowing like before by dragging the two points on the graph horizontally and vertically with the left mouse button. Windowing with the right mouse button is still possible.

Volume Rendering
You can visualize a dataset in 3D without segmentation efforts. This powerful visualization tool instantly gives you a 3D view of your dataset’s content.

Enhanced Rotation and Translation tools
New tools for Rotating and Translating STL’s and 3D objects enable straightforward positioning of the objects in your project. All you have to do is grab the rotation or translation tool.

New Shortcuts
New shortcuts were added to the software General Shortcuts SPACE If you hover with the mouse over a view and press the spacebar, that view is put to full screen. To unzoom to full screen, press the spacebar again. If you want to make all masks invisible, press CTRL+I. To make all previous visible masks visible again, press CTRL+I again. With the scroll wheel you can zoom in on the active view.

CTRL +I

Scroll wheel

Navigation shortcuts for the 3D view Arrows keys Rotate the 3D view left/right and up/down PageUp Rotate the 3D view 30 degrees up PageDown Rotate the 3D view 30 degrees down Home Rotate the 3D view with 30 degrees left End Rotate the 3D view with 30 degrees right SHIFT + keys above ALT + left/right Pan the 3D view Do washing machine rotation

Extended Clipping
The extended clipping functionality enables you to manipulate several clipping planes at the same time. It also gives you greater input on the actual clipping action. These new visualization options expand the possibilities for

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displaying your 3D images

Convert MedCAD object to mask
MedCad Object like spheres, cylinders and nerves can be converted to a mask.

Add Annotations
With Mimics 10 you can make annotations directly on any object and save this additional information in the dataset. This new functionality ensures efficient communication among all parties involved in the project.

3D Mask Editing
The new 3D mask editing tool allows users to display the 2D mask information in the 3D view and edit that mask in 3D. This tool is very helpful when removing scatter and for easily separating complex structures like vessels.

Delete unselected images from project
After you’ve imported the images, you can still choose to delete unselected images in the organize image dialog.

MedCAD Module
Fit Centerlines
Using Mimics 10 you can calculate and measure the centreline of 3D object, for example of a vessels. This information can then be used for clinical trials, diagnostic purposes or for the design of new or custom devices.

FEA Module
New Ansys Format
You can now export you optimized surface mesh as an Element Based Ansys mesh. Starting from this mesh format you can immediately generate your volume mesh in Ansys.

Simulation Module
New Cutting Tool
A new cutting tool was added to the simulation module. By drawing a curve on a 3D object, you can separate the enclosed object from the original 3D object.

Soft-Tissue Module
The Soft-Tissue tool predicts the behavior of the facial tissue with regard to the surgical bone repositioning. The Soft-Tissue module is based on a biomechanical model of the soft-tissue and it runs on top of the simulation module.

Installing Mimics

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We recommend that you close all other applications before installing Mimics. You must have administrative privileges to install the software. Place the Mimics CD into your CD-ROM drive. Make sure the artwork faces up. The autorun starts automatically. If the autorun does not start automatically, browse to your CD-drive and choose autoplay or double-click on ‘MimicsSetup.exe’ in the Mimics folder. During the installation the following dialogs will be shown:

STEP 1:

Wait until the progress bar is finished. You will automatically go to step 2.

STEP 2:

Click Next to proceed.

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STEP 3:

After reading the license agreement, select the “I accept the terms of the license agreement” bullet and click on the Next button.

STEP 4:

Select your region and click Next.

STEP 5:

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Introduction Page 8 of 21 Choose for the Complete or Custom setup type and select where Mimics will be installed. click on the Browse button and select an existing directory out of the list.0\ by default. you will immediately go to Step 7. If you have chosen the Complete setup.htm 2/3/2014 . STEP 7: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. If you prefer another directory. If you have chosen the Custom option. Mimics will be installed in C:\Program Files\Materialise\Mimics 10. you will go to Step 6. Click Next to proceed. STEP 6: Select if you want to install the Demo Files or not and click on Next.

Mimics will store the studies in a folder C:\MedData by default. you can choose where these demo files should be installed. If you want another folder name.Introduction Page 9 of 21 If you have chosen to install the Demo Files. If you want to change this directory.htm 2/3/2014 . STEP 9: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. then type a new name or select one from the existing folder list. STEP 8: Program icons will be added to the Programs Folder > Materialise Software. select Browse and go to the folder where you want to store your data.

htm 2/3/2014 . click Next to proceed. This window will close automatically when the progress bar is finished. If you want to change or review something. STEP 10: The Mimics software gets installed. STEP 11: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE.Introduction Page 10 of 21 When everything is filled in like you want. This can take a few moments. click Back.

htm 2/3/2014 . Click Finish to close the installation dialog. go to Start > Settings > Control panel > Add/Remove programs. on your desktop or go via the Start button to Programs. To display the Registration dialog. To uninstall Mimics. Materialise Software is password protected. Registration To start Mimics. Mimics can be registered with a local license or a floating license. go to the Options menu and choose file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE.Introduction Page 11 of 21 Mimics will then ask you if you want to see an overview of what the new features are in Mimics. It’s recommended to reboot your computer to finalize the installation. Note: The installation of the DICOM Input Application and of the Distractor and Anthropometric template libraries are separate processes.0 and click the Remove button. request passwords and register new modules. STEP 12: The software is successfully installed. a registration dialog will appear. Select Mimics 10. The libraries have to be installed separately in order for the Simulation module to function correctly. double click the Mimics icon Materialise and choose to start Mimics. display contact information. All Mimics folders and the desktop icon will be removed. When you start Mimics for the first time or when your password has expired. In the Registration dialog you can display your current license situation.

When you click on the Contact information button. you will see contact information so you can contact Materialise if needed. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. Register new modules There are three different steps when registering new modules: Step 1: Request password You can request password via the Password request wizard. click on the Request password button. There are two sections in this dialog: the Register new modules section and the System Information section. To start this wizard.htm 2/3/2014 .Introduction Page 12 of 21 Licenses.

you can enter this in the Password edit box. You will then see a message that gives you feedback about the registered passwords. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. you can register the password by clicking on the Register button. your CCKey (if filled in) and you can specify floating license servers. Step 3: Register When the password has been entered in the edit box. System Information In the System Information section of the register dialog you can find your SystemID. Passwords that have been copied to the clipboard can be pasted in the edit box by clicking on the Paste button.Introduction Page 13 of 21 Step 2: Enter password When you have generated a password via the Password request wizard.htm 2/3/2014 .

You can add or change floating license servers by clicking on the Specify button in the System information section. but we advice you to do this because this will facilitate the password generation process. This function should only be used when you have floating passwords. CCKey The CCKey is a unique identifier for your software license.Introduction Page 14 of 21 System ID Your SystemID is a unique identifier for your pc. It is optional to fill in the CCKey. You can use this key for generating passwords with our on-line password generation system. The CCKey can be found on your Certificate of Authenticity that you will receive when you buy the software (so evaluators don't have a CCKey). This id is dependant on your hardware and will be used to generate a password.htm 2/3/2014 . This will open following dialog: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. Floating license server Via the specify button you can enter floating license servers if needed.

The name. IP Port and Description for the floating license server. Show Modules When you click on the Show Modules button. click on the Add button. there will appear n/a as number of days left and "no license found for this module" will be displayed under the comments section. all the floating license servers that are used by the software are listed. If you haven't got a password for a certain module.Introduction Page 15 of 21 In this dialog. For each floating license server the IP Address (or hostname). you will see a list of all the modules that are available for your software. select the server in the list and click on the Change button.htm 2/3/2014 . With the browse function you can browse your Network Places. You can also Browse for a server by clicking on the Browse button. select the appropriate floating license server and by clicking on the OK button. the name of this server will be filled in automatically. days left and a comment is displayed for each module. These buttons will open following dialog: In this dialog you can fill in the IP Address or hostname. type of license. the port and a description are displayed. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. To add a new floating license server. select the server and click on the Delete button. To remove a floating license server from the list. version. To change a floating license server.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. If you have bought our software. we advice you to use the Online password generation. You can choose between Online password request. This way you will receive your passwords instantly. Request passwords via E-Mail and Request passwords via Fax. if you have already received your Card of Authenticity and if you are connected to the Internet. you can choose how you want to request your passwords.htm 2/3/2014 .Introduction Page 16 of 21 Password Request Wizard When you start the password request wizard.

You will receive this Certificate of Authenticity when you buy the software. This CCKey can be used to generate your own passwords via the online password system. You can find your CCKey on your Certificate of Authenticity. This card contains a unique CCKey that identifies the license you have bought. First you will have to choose your language by clicking on one of the flags. If you have filled in the required information you can click on the Finish button and you will automatically be directed to the correct webpage.htm 2/3/2014 . you will be asked to fill in your CCKey and E-Mail address if this data hasn't been entered before.Introduction Page 17 of 21 Online Password Request When you have chosen to generate passwords online. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE.

htm 2/3/2014 .Introduction Page 18 of 21 You can find more information about web passwords by clicking on the How does it work? link. When you have chosen your language you will go to the second screen where you have to fill in your CCKey. If you have entered your CCKey in your software when asked. this key will already be filled in automatically. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE.

your E-Mail software will start and a new mail will be shown with all the information needed for us to generate a password. you won't have to fill in your contact data again. This password can be used for a week and should be requested when your password has expired and you really need to continue working with the software. So next time you request a password. This password will be sent to you by E-Mail. this information will be saved.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. you will see a window where you have to fill in your contact data.Introduction Page 19 of 21 To continue click on the Login link. When this is done. you can generate an emergency password if needed. In the next screen you will have to fill in information about the software you are requesting passwords for. Request Passwords via E-Mail When you choose to request a password via E-Mail. you can request a regular password or an emergency password. Fields with an exclamation mark behind them have to be filled in. When you have filled in the correct information and click on the Finish button. If you request a regular password and you receive a message that some of the information was not correct and that you will be contacted by Materialise. Once you have filled in your contact data.

and explains procedures for most tasks.Introduction Page 20 of 21 Request Password via Fax When you choose to request a password via Fax.htm 2/3/2014 . The Help window consists of a tabbed window showing a tree of topics at the left side and a preview window at the right side. To get help. maximize the help window or scroll with the scroll bars. a document will be shown with all the information needed for us to generate a password. Fields with an exclamation mark behind them have to be filled in. The help pages contain a description of each command and dialog box. This document can then be printed and faxed to us. press F1 or select Help | General Help from the menu bar. If the page is not displayed completely. you will see a window where you have to fill in your contact data. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. When you have filled in the correct information and click on the Finish button. Once you have filled in your contact data. Using help Mimics provides Help so that you can get useful information while you are working. So next time you request a password. you won't have to fill in your contact data again. this information will be saved.

The tree will be updated accordingly. Click the Display button to view the item that is highlighted. Select the Index tab and type the first few letters of the topic you're looking for. Click on an item in the list to view the page. To hide the contents window. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh88DE. Once it's hidden you can show it again by clicking again on this button. To print the current page. To search very quickly all pages about a specific topic. The corresponding items will be highlighted in the list while typing.Introduction Page 21 of 21 You can search for the correct help page in 4 different ways:     Browse through the tree by clicking on the book icons and page icons. To display the previous page. To display the page that was shown before clicking the Back button. click on the Search tab and fill in the name of the topic.htm 2/3/2014 . Click on an underlined item in the preview page to jump to the help page about that item. Click the List topics button to show a list of all help pages about the topic.

The upper left view (surrounded by an orange border) shows the coronal images that are the images resliced in the XZ-direction (Front-view). the compression of the project is displayed. The lower right view (surrounded by a light-green border) shows the 3D view.htm 2/3/2014 . There are several different types of compression possible: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. The lower left view (surrounded by a green border) shows the sagittal images that are the images resliced in the YZ-direction (Side-view). The images in the top right view are called the axial images (XY-view or Top-view) and are surrounded by a red border.The different views Page 1 of 27 The different views In the default configuration the images appear in a four-dimensional engineering view. These windows can be resized by moving the edge between the images (Click and drag to move this edge). Image Axial Sagittal Coronal 3D view Parallel Cross-sectional Color Red Green Orange Light-green Yellow (these images are only visible after performing an online reslice) Blue (these images are only visible after performing an online reslice) The other images that can be shown are:   Alignment image (if available) X-ray image Title Bar The title bar displays some information about the project: The name of the project is displayed first (unless you have chosen to hide the patient name) and after the patient name.

in the 3D toolbar to toggle between file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. Corresponding to some of these functions. Toggle transparency You can show the 3D object opaque or transparent.The different views Page 2 of 27 Displayed in title bar: Lossless Compression CT Compressed MR Compressed Lossy JPEG Compressed Lossy JPEG & CT Compressed Lossy JPEG & MR Compressed Case: No compression was used while importing and JPEG compression was not used during saving CT compression was used while importing and JPEG compression was not used during saving MR compression was used while importing and JPEG compression was not used during saving No compression was used while importing and project was saved with JPEG compression CT compression was used while importing and project was saved with JPEG compression MR compression was used while importing and project was saved with JPEG compression Menu Bar Almost all functions can be accessed via the menus of the menu bar. you will find buttons on the toolbars. Click on the button opaque and transparent view.htm 2/3/2014 . 3D Toolbar The 3D toolbar is displayed at the right side of the 3D view.

to evaluate the gray values on the section boundaries or to look inside the model to get a better comprehension of the geometry. make sure to check the active icon . To enable clipping click on the Enable/Disable clipping button in the clipping tab: . When you rotate the 3D along the clipped plane. Drag the Transparency slider at the bottom of the 3D properties dialog. Several clipping planes can be activated at the same enabling you to isolate the part of interest. Clipping in the Axial Clipping in the Sagittal Combined axial and Plane Plane sagittal clipping plane The position of the clipped plane in the 3D view corresponds with the position of the active axial. It can be used. The settings of the clipping can be changed Active By default one axial clipping plane is active. the 3D surface is opaque and nothing below the surface can be visualized. the visibility file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. the 3D surface is completely transparent. sagittal or coronal image. To make more planes active. coronal and sagittal.htm 2/3/2014 . axial. The section can be made along the different planes. If the slider is all the way to the left. Scrolling through the 2D images updates the clipped plane in 3D.The different views Page 3 of 27 Transparency off Transparency on You can change the transparency of the 3D object and make objects transparent. Clipping Clipping allows you to visualize the section in which you are interested. If the slider is all the way to the right. Also navigation on the clipped 3D is possible by clicking on visible parts on the 3D.

To check your rendering option.The different views Page 4 of 27 automatically reverses. Click on the clip icon to lock to a clipping direction or to unlock. Note: This technique is only available in OpenGL and direct3D rendering (not in software). you can determine the location of the clipping plane with the slider at the bottom of the clipping tab. . only the 3D Object is clipped and you can see inside the 3D Object. For each of the clipping planes. Texturing You can also choose between three texturing methods: No texturing Object texturing Full slice texturing When choosing No texturing.htm 2/3/2014 . All objects are Clipping along two axial and a sagittal Clipping along the axial and sagittal plane plane Clip By default the direction of the clipping plane is defined by the viewing angle. When choosing Object Texturing. you can choose which objects need to be clipped. go to Option | Preferences and select the OpenGL or Direct3D rendering option in the 3D file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. but the whole 2D slice is visible in the 3D window. The direction of the clipping plane can be locked by selecting a clip direction. disable the lock icon . a texture corresponding with the 2D slice is placed in the contours of the 3D Objects. When choosing Full slice texturing. Lock The location of the clipping plane is locked to the slice position. To unlock the clipping plane from the slice position. You can choose this by selecting the clipping plane in the list and changing the selections in the dropdown menu selected by default. For each view you can define two clipping planes. Type As stated above you can select multiple clipping planes. the 3D Object is not clipped. When the lock icon is disabled.

Volume rendering is a pure visualisation tool and cannot be used for anything else (e. The transparency of the gray values is set by the opacity lines on the histogram. Volume rendering Volume rendering allows you to quickly visualise your 2D image data as a 3D object without any segmentation. You can find the interface for the volume rendering in the volume rendering project management tab: Defining the opacity This interface shows a histogram which represents the gray values or Hounsfield units of the dataset. The transparency of the voxels is determined based on their grey value. Subsequently the voxels are represented transparent. activate the hardware acceleration in the same dialog. exporting). In the first column the line representing the low Hounsfield values is positioned to the bottom. The 3D object is build up out of the voxels representing the dataset.g.The different views Page 5 of 27 settings. The higher a line is positioned the more opaque the voxels within that range will be visualised. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.htm 2/3/2014 . In the second column the line is positioned higher which makes the voxels opaque. To accelerate the performance of clipping.

The predefined settings are optimized for CT image and allow you to quickly select bone. moving and deleting bullets is available as for the opacity line. Predefined settings On the bottom of the volume rendering interface you find a dropdown list with predefined settings. Only the reference planes of the views that are displayed can be shown in the 3D view. The same system for adding.The different views Page 6 of 27 Move a point Add a point Position a point click left and drag the point to its new position Click left on a line to add an extra point Delete a point Right click on a point and select delete to delete a point Defining the color The graph below the histogram defines the color of the rendered voxels. To delete your predefined setting. select it from the dropdown box and click on the delete button. You can choose a color for each point in the graph by right-clicking on the points and choosing Change Color. The reference planes take over the colors that belong to the different views: Axial Red Coronal Orange Green Sagittal Cross Sectional Blue Parallel Yellow The reference planes that have to be shown can be selected in the 3D tab of the Preference settings. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. Mimics will then create an interpolated shading between the different control points.htm 2/3/2014 . soft-tissue or both You can save your current setting as a predefined setting by clicking on the save button. Show reference planes It is possible to show in the 3D view the reference planes of the current position by clicking on the Show Reference Plane button .

Selecting an item from this list will position the 3D object according to the selected position.htm 2/3/2014 . a list with all possible default views is displayed. Rotate view The rotate function is only available on a 3D object. There are different ways to select the rotate function:       right-drag with your mouse button use the arrows-keys for precise rotation use Home / End to rotate 10 degrees Left / Right use Page Up / Page Down to rotate 10 degrees Up / Down right-click in the 3D view and select Rotate View from the context menu click on the Rotate View button in the toolbar file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.The different views Page 7 of 27 Select 3D view When you click on Select 3D View button .

select its entry in View menu > Indicators. The set of orange tick marks to the left of the axial images reference the position of each coronal image in the study. For every 3D object in the project there is a corresponding cube. visible or invisible. In this dialog you can make your selection of these indicators.The different views Page 8 of 27  select View > Rotate View from the menu bar Toggle visibility By toggling the colored cubes in the 3D toolbar. you can make the 3D objects. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.htm 2/3/2014 . If you never want to see one or more indicators when loading a project. Tick Marks The set of red tick marks to the left of the sagittal and coronal images reference the position of each axial image in the study. select Preferences from the Options menu and go to the Visualization tab. tick marks. with the corresponding color. slice positions and orientation strings. tick marks or slice positions. Indicators in the views On the different views you can see intersection lines. The set of green tick marks below the axial images reference the position of each sagittal image in the study. To hide the intersection lines. Select again its entry to show it again.

In the other views. It references the exact location of the axial image. Slice Position In the view that contains the scanner images. The middle blue line references the exact location of the cross-sectional image (surrounded by a blue border). Intersection Lines In the View menu. go to Options > Preferences > Visualization. Notice the red horizontal line across the sagittal and coronal images. After performing an online reslice. the slice position is indicated in the lower right corner. you will see 3 blue dashed or full lines and a yellow dashed or full line in the axial image. When you move to a new position. the slice position is indicated in the lower left corner and the image number is indicated in the lower right corner.The different views Page 9 of 27 tick marks on tick marks off In the View menu. the intersection lines will be updated and show you your current position in the data set. The most right blue line reference the exact location of the cross-sectional image at the right bottom corner of the cross-sectional grid. Image Axial Sagittal Coronal Numbering Increasing from bottom to top Increasing from the right to the left side of the patient Increasing from posterior to anterior Orientation strings file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. Color Table Axial Cross-section Parallel Sagittal Coronal Red Blue (only visible if the project is resliced in Reslice Layout) Yellow (only visible if the project is resliced in Reslice Layout) Green Orange Note: You can choose between dashed or full lines in the Visualization tab of the Preference window. The relation between the different views is indicated by the colors of the intersection lines (dashed or full colored lines over the view). If you prefer another setting permanently. When you move to a new position. the intersection lines will be updated and show you your current position in the data set. the preference setting for intersection lines can be temporarily overruled. If you prefer another setting permanently. The most left blue line reference the exact location of the cross-sectional image at the left top corner of the cross-sectional grid. They are in the matching color of the corresponding view. The yellow line reference the exact location of the parallel image that is displayed. go to Options > Preferences > Visualization. the preference setting for tick marks can be temporarily overruled.htm 2/3/2014 .

By clicking once on an image (e. The functions in the context menu can differ.htm 2/3/2014 . Pan view Every image and 3D view can be panned or moved. a STL. The Context Menu If you right-click with your mouse on any of the views.g. you will see the context menu.The different views Page 10 of 27 The colored letters located on each view shows the orientation of the images. There are different ways to select the pan function:     hold down the SHIFT key.. When you select the pan function. right-drag your mouse button right-click in an image or in the 3D view and select Pan View from the context menu click on the Pan View button in the toolbar hold down the SHIFT key in combination with the arrows-keys for precise rotation file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. the cursor will change to a cross-shaped double arrow.. the axial image) with your left mouse button all images are immediately updated to show the same point. . depending on the location you click on: if you right-click on an image. There are several easy shortcuts available from the default context menu: Pan View Zoom Unzoom Zoom to full screen 3D Window Enables the panning mode Enables the zoom mode Unzooms the view Zooms the view to full screen Enables the 3D view in the window 1-Click Navigation 1-click navigation is very easy. if not you can easily change them in the Change Orientation window going to File > Change Orientation. on a 3D object. P : Posterior A : Anterior L : Left R : Right T : Top B : Bottom Looking at the images you can verify if they are correct. on the 3D view. Navigation is also possible from the 3D image. a CAD object.

There are different ways to select the rotate function:        right-drag with your mouse button use the arrows-keys for precise rotation use Home / End to rotate 10 degrees Left / Right use Page Up / Page Down to rotate 10 degrees Up / Down right-click in the 3D view and select Rotate View from the context menu click on the Rotate View button in the toolbar select View > Rotate View from the menu bar There are two different modes when rotating the 3D view. When your mouse cursor is in the middle of the 3D window and you then hold down the right mouse button. When your mouse cursor is at the side of the 3D window and you then hold down the right mouse button. drag and release to indicate the opposite corner.htm 2/3/2014 .The different views Page 11 of 27   Hold down the SHIFT key in combination with Home / End for quick Left / Right panning select View > Pan View from the menu bar Rotate view The rotate function is only available on a 3D object. Click on the left mouse button to indicate a corner of the zoom rectangle. the 3D view turns about a vertical axis when you move the mouse left and right. The 3D view tilts around a horizontal axis if you move the mouse up and down. the 3D view rotates around an axis perpendicular to your screen when moving the mouse. Zoom Allows to Zoom in at a user defined rectangle. Can be used on every image. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.

Zoom to full screen Allows you to display a view on the whole screen. To return to a normal view. You can also zoom to full screen by by invoking the context menu by right-clicking on the view. You need to select the function first and then left-click on the view on which you want to apply the function. Zoom to fixed factor Allows to Zoom in at a defined factor. Unzoom Changes the display scale to show the whole image. click again on the Zoom to full screen button.htm 2/3/2014 . Click on the arrow and choose from the drop-down list the factor you want to zoom with: your cursor becomes a lens. Project Management file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. To unzoom press the spacebar again. right-drag your mouse button right-click in an image or in the 3D view and select Zoom from the context menu click on the Zoom button in the toolbar select View > Zoom from the menu bar Note: The behaviour of zooming is different in Reslice Layout.The different views Page 12 of 27 There are different ways to select the zoom function:     hold down the CTRL key. Click on the Zoom to full screen button and the cursor will change to a magnifying glass. Then click on an image. Zoom to full screen on axial view When you hover with the mouse over a view and click on the spacebar the view is put to full screen.

The project management consists out of containers which hold a number of tabs.The different views Page 13 of 27 The project management gives you an overview of all the objects in the project. Each tab stands for a kind of objects in Mimics. To enlarge them you can undock them by left-clicking on the pointed top of the container and dragging the container outside the project management. On the bottom of a tab you have a toolbar with the most common functions. You can left-click on the tab and drag the tab outside the container.htm 2/3/2014 . The volume rendering tab shows a histogram of the dataset and a line which allows you to set the opacity of the voxels. a delete and a properties button. This button lists all the functions that can be performed on the selected object. The contrast tab allows you to adjust the gray scale of the images. The same counts for the different tabs. It lists the available objects in the project. Tabs can as well be dragged to another container Masks file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. On the toolbar you typically find a create. The clipping tab lists the possible clipping planes and their settings. The last button on each toolbar is always the action button . Besides object based tabs there are three different tabs on the bottom of the project management. When the containers are docked in the project management they have a fixed size. You can hide the project menu by toggling the project management button in the main toolbar .

Functions on masks New Delete Properties Duplicate Clear Calculate 3D Action Creates a new mask with a default threshold Deletes the selected mask Gives numerical information of the selected mask Duplicates the selected mask Clears the contents of the selected mask. STL. List of the created masks Name Visible Lower Threshold Higher Threshold Name of the mask. Lower Threshold setting of the mask.The different views Page 14 of 27 A mask is a collection of pixels where all actions (editing. . By clicking on the name of the mask. the threshold of the mask is kept Opens the Calculate 3D window Lists the available function on the selected mask Properties The mask properties gives numerical information about the gray values in the selected mask: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. . region growing.htm 2/3/2014 . it can be renamed. Lists if the mask is visible or not by means of glasses... Higher Threshold setting of the mask.) are based on.) and calculations (3D calculations.

htm 2/3/2014 . 3D objects List of the created 3D reconstructions file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.The different views Page 15 of 27 Minimum value Maximum value Average value Standard deviation Minimum gray value in the selected mask Maximum gray value in the selected mask Average gray value from the selected mask Number of pixels Mask volume Scale Amount of pixels in the selected mask The volume of the mask The scale you are working in: GV (Grayvalues) or HU (Hounsfield Units).

medium and high. custom. the transparency button has to be enabled. Quality which was set before calculation. possible options are: opaque (= not transparent). Deletes a 3D.htm 2/3/2014 . it can be renamed. To see your objects transparent. Lists the transparency settings of the 3D. low. You can change the visibility of the contours by clicking on the glasses.The different views Page 16 of 27 Name Visible Contour Visible Transparency Name of the 3D. Change the transparency by clicking on the icon in the transparency column. Gives the properties of the calculated 3D object. Quality Functions on 3D reconstructions New Delete Properties Move Rotate Action Creates a new 3D. high. Lists if the contour of the 3D object is visible on the 2D images or not by means of glasses. The Calculate 3D window appears. Activates the handles to move the STL to a new positions Activates the handles to rotate the STL around its axis Lists the available functions on the selected 3D object Properties of a 3D Object When you click on the Properties button in the 3D Objects list. medium. Lists if the 3D is visible or not by means of glasses. by clicking on the name of the 3D. possible options are: low. following dialog box will open: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.

htm 2/3/2014 . Opaque 3D Transparent 3D If the Details button on the 3D Properties dialog is selected. the 3D surface is completely transparent. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. The volume. surface. you need to click the Toggle transparency button in the 3D toolbar. You can change the transparency of the 3D object and make objects transparent. color and transparency of the object. Drag the Transparency slider at the bottom of the 3D properties dialog. If the slider is all the way to the right. If the slider is all the way to the left. which give a good idea if reducing of the file for further applications is needed. the 3D surface is opaque and nothing below the surface can be visualized.The different views Page 17 of 27 Mimics displays the name. In order to see the 3D object transparent. outer dimensional parameters and the number of points and/or triangles are also shown. some measurements of the 3D object are displayed.

You can also rotate the object around an axis perpendicular to the camera by grabbing the outer ring of the rotation tool. Rotate When you select a 3D object and click on the Rotate button. These buttons allow you to rotate and/or move one or more 3Ds. The rotation value is shown in the status bar. The translation value is shown in the status bar. grab and move the middle of the tool.htm 2/3/2014 . Move When you select a 3D object and click on the Move button. two new buttons will appear on the 3D tab of the project management: Move and Rotate. To change the rotation center select the center of the tool and move it to its new position. You can now rotate the 3D objects around the X. rotation handles will appear around the 3D object. To translate the object parallel to the viewing plane. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. translations arrows appear. Y or Z axis of the project by grabbing one of the colored rotation handles. To translate the 3D object grab a translation arrow and move the mouse.The different views Page 18 of 27 Move and Rotate button When the simulation module is licensed.

Functions on Polyline sets New Delete Duplicate Color Polyline growing Action Creates a new polyline set. Lists if the polyline is visible or not by means of glasses. The Calculate Polylines window appears. By clicking on the name of the polyline.The different views Page 19 of 27 Polylines List of the created Polyline sets Sets Visible Based On Name of the polyline. Lists the available functions on the select polyline set STLs file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. it is independent of a mask. it can be changed. If the set is grown out of another set.htm 2/3/2014 . Deletes a polyline set Duplicates the selected polyline set Changes the color of a polyline set The polyline Growing tool provides the capacity to create several sets of polylines. Tells on which mask the polylines were calculated.

it can be changed. written out by Mimics when reslicing or file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. Displays the properties of the selected STL file. You can change the visibility of the contours by clicking on the glasses. Lists the available functions you can perform on the selected STL Opens the transformation dialog: In this dialog. Lists if the contour of the object is visible on the 2D slices or not by means of glasses. you can enter a transformation matrix. possible options are: opaque (= not transparent). you can move the STL in the 2D views and the 3D view. Functions on Objects Load Remove Properties Export STL Move Rotate Action Transform Loads an STL file into the project. low. When the Rotate button is enabled.The different views Page 20 of 27 List of created Objects Name Visible Contour Visible Transparency Name of the object. When the Move button is enabled. Saves the selected STL file (with its current position). invert the transformation matrix if needed and apply it on the selected STL file.htm 2/3/2014 . you can rotate the STL in the 2D views and the 3D view. Lists the transparency settings of the STL. medium and high. Lists if the object is visible or not by means of glasses. You can also load a transformation matrix file. Removes an STL file from the project. the transparency button has to be enabled. Change the transparency by clicking on the icon in the transparency column. By clicking on the name of the object. To see your objects transparent.

a 2D or 3D angle or a density measure. a 3D distance.The different views Page 21 of 27 cropping a project or when doing an STL registration. Lists the available function on the selected measurment Delete Properties Locate Action Curves file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. These are the same measures that are available in the tools toolbar and are represented in the list with the same icon. Visible Value Deviation Area Functions on Measurements New Shows a menu from where you can choose the type of measure. The area in mm² of a density measure. Possible measures are: a 2D or 3D distance.htm 2/3/2014 . Measures List of the created Measurements Type The type of measure. These are the same measures that are available in the tools toolbar. a 2D angle. Depending on the type of measure this value can represent a distance (mm). Only angle and distance measures can be located. Possible measures are: a 2D distance. Lists if the measure is visible or not by means of glasses. represented by its corresponding icon. Deletes one or more measures. The deviation in Hounsfield units or grey values for a density measure. Updates all views to show to selected measure. a 3D angle or a density measure. an angle (in degrees) or a mean density (HU or grey values). Shows the properties of the selected measurement.

it can be changed. The resliced images can only be viewed when the Reslice layout is chosen in the View menu. Deletes one or more reslice curves. To draw a reslice curve.The different views Page 22 of 27 A reslice curve allows you slice the images in a different direction. Annotation List of the created Annotation Name Name of the annotation. Functions on Curves New Delete Opens the reslice curves toolbox to draw a new curve. but can be altered by double-clicking on the Optimal text. The cross-section length determines the width of the cross-section images. set 0 as the value of the cross-section length. The name is generated automatically based on the object on which the annotation is attached file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. select Online Reslice from the File menu. This length is set to optimal by default. The active reslice curve is indicated by means of glasses. This way you can specify an exact cross-section length. By clicking on its name. List of the created Curves Name Visible Cross-Section Length (mm) Name of the reslice curve.htm 2/3/2014 . In the Reslice layout the images corresponding the active reslice curve will be shown. Note: To return to the Optimal setting after you have specified an exact length.

The different views Page 23 of 27 Visible Object Text The visibility of the annotations is set by means of the sunglasses Lists the object to which the annotation is attached Shows the content of the annotation Functions on Annotations New Activates the annotation cursor.htm 2/3/2014 . Delete Properties Locate Action Deletes the selected annotation Opens the Annotation Properties dialog Updates all views to show to selected annotation. The annotation properties dialog will open in where you can add your comments. Click with your mouse on the object on which you want to attach an annotation. You can as well define the position of the points by filling in a value in the Minimum and Maximum field. When your display setting is set on true color (24-bit or 32-bit) you will be able to map the pixel values onto 128 gray levels. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. You can change the window by grabbing one of the points or the line and move it with the left mouse button. Lists the available actions on the selected annotation Adjust grayscale The mapping of pixel values into gray levels is specified by the level and the width of the line on the histogram. The amount of available gray values levels is dependent on your display setting.

You can find more information about clipping in the 3D toolbar section file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.this heightens the contrast within the soft tissue. Clipping In the clipping tab you can define the different clipping planes and their options. Move the mouse down to increase the width of the gray scale . Move the mouse to the left to decrease the level of the gray scale . All the images are updated immediately with the new gray scale. Volume rendering The volume rendering tab shows a histogram of the dataset and a line which allows you to set the opacity of the voxels.this lightens the soft tissue.htm 2/3/2014 . Move the mouse to the right to increase the level of the gray scale this darkens the soft tissue. you can choose one of the predefined scales from the dropdown box. To activate clipping select the clipping button in the 3D toolbar. When you are satisfied with your gray scale. To visualize the volume rendered 3D select the volume render button in the 3D toolbar. release the mouse button. The cursor will change into .The different views Page 24 of 27 Instead of defining the contrast yourself. You can change the gray scale also interactively by pointing at an image of interest and dragging the right mouse button.this lowers the contrast within the soft tissue. Move the mouse up to decrease the width of the gray scale . You can find more information about volume rendering in the section about the 3D toolbar.

Move the mouse vertically to change the width of the gray scale.htm 2/3/2014 . SHIFT + Right mouse button CTRL + Right mouse button Zoom: Move the mouse vertically while keeping the buttons pressed to zoom in and out. that view is put to full screen. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F. To unzoom to full screen. Pan: Move the mouse while keeping the buttons pressed to pan. press the spacebar Shortcuts on files CTRL + O CTRL + P CTRL + S CTRL + N Open a file Print a file Save a file Close a file Shortcuts on the views ArrowUp ArrowDown PageUp PageDown CTRL + L Right mouse button Go to next slice Go to previous slice Go 10 slices up Go 10 slices down Make slice indicators visible/invisible Adjust gray scale: Move the mouse horizontally while keeping the buttons pressed to change the level of the gray scale.The different views Page 25 of 27 Shortcut Keys General Shortcuts F1 CTRL + Z CTRL + Y CTRL + F CTRL + I CTRL + SHIFT + M Alt + F4 SPACE Open the Online Help Undo last action Redo last action Enable/Disable the Navigation Toolbar Makes all mask invisible Enable/Disable the Movie export Exit Mimics If you hover with the mouse over a view and press the spacebar.

The different views Page 26 of 27 Shortcuts on the 3D view Arrow keys Page Up Page Down Home End SHIFT + keys above ALT + left/right Rotate the 3D view left/right and up/down Rotate the 3D view 10 degrees down Rotate the 3D view 10 degrees up Rotate the 3D view 10 degrees left Rotate the 3D view 10 degrees right Pan the 3D view Do washing machine rotation Shortcuts on the layouts F2 F3 F4 F5 Image Layout 3D Layout Reslice Layout Simulation Layout (if the simulation module is licensed) Shortcuts on Segmentation functions Region Growing CTRL + R Start the Region growing function Edit CTRL + E While in edit mode: D E T CTRL + drag left mouse button SHIFT + Left mouse button Open the edit toolbar and go in edit mode Draw Erase Draw with local threshold Resize the edit cursor Temporarily release the edit-tool and do 1-click navigation. Shortcuts on text fields in dialogs CTRL + C CTRL + X CTRL + V Copy Cut Paste Shortcuts on Movie Tool CTRL + SHIFT+ M SHIFT+ F8 SHIFT+ F9 Start the movie tool Start Recording / Stop Recording Pause Recording file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.htm 2/3/2014 .

but subtle differences in the soft tissue cannot be visualized. one of the pioneers in computerized tomography. If you narrow the gray scale. The extent of the gray scale is specified by its width. Using this scale. Narrowing the gray scale can help you locate the mandibular canal if it is not easily seen with the default gray scale. The pixel values are scaled so that the linear X-ray attenuation coefficient of air equals -1024 and that of water equals 0. Mimics displays the CT images using up to 256 gray levels if your display setting is true color (24-bit or 32-bit). fat is around -110. a level of 0 specifies that water will be displayed as mid-gray. The mapping of pixel values into gray levels is specified by a level and a width. The pixel values are shown graphically by a set of gray levels that vary linearly from black to white. trabecular bone is in the range of 100 to 300 and cortical bone extends above trabecular bone to about 2000. you can better visualize subtle differences in the soft tissue or trabecular bone. muscle is around 40. but at the cost of forcing cortical bone to be in one gray level: white. For example. A gray scale is centered about its level.The different views Page 27 of 27 Shortcuts on Polylines CTRL + U Update polylines CT Gray scale CT images are a pixel map of the linear X-ray attenuation coefficient of tissue. The default gray scale used by Mimics allows you to see the full range of tissue from air in the maxillary sinus to the densest of cortical bone. 128 gray levels if your display setting is 256 color palette. This scale is called the Hounsfield scale after Godfrey Hounsfield. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh704F.htm 2/3/2014 . but as few as 32 gray levels if your display setting is high color (16-bit).

When you click on the black arrow on the Open project button. a list of previously opened projects appears.File Menu Page 1 of 74 File Menu The file menu contains the following items: You will also find the corresponding buttons in the toolbar. is enabled. Folders for the floppy-. The Open project dialog displays your folders containing Mimics files (*. Click on a folder to see the list of Mimics files in that folder.mcs) on the left side of the window. Hide file name. Use the arrows on the scroll bar if the patient you wish to view is not displayed. To change the Hipaa preferences go to preferences. Compact Disc and zip-drive are also displayed when they are installed. There are two different modes in the Open project window. Open a study by clicking once its line in the list and then the Open button or by double-clicking its line.htm 2/3/2014 . The second mode will show you more information for each project. The first mode allows you to easily browse on your harddisk. you can change the Hipaa settings in the General section file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Note: The first mode will be disabled when the Hipaa preference. You can switch between these modes with the button. Open project Open an existing project by selecting File > Open project from the menu bar or by clicking its button on the Main Toolbar.

You will be asked if you want to add the folder to the list of favorites. To delete the selected study from your computer. Shows all the projects in the folder and subfolders Switches between the two browse modes. To select a new directory in order to see the reformatted CT studies the folder contains.File Menu Page 2 of 74 List of studies Browse tree Patient Study ID Study Date File Displays the browse tree Displays the patient name Shows the study ID Shows the study date Displays the file name Functions Add directory to Favorites Make default Delete folder Browse Delete study Search in Subfolders Switch view Sort by column Change column order Open Cancel Adds the current Makes the selected folder your default To delete the selected folder from the list of favorites. Quickly sort the studies by a column by clicking on the column header Change the order of the columns by dragging the column header to the left or the right Click on the Open button after selecting a study or double-click on a study to open it Closes the Open dialog box file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm 2/3/2014 .

A reduction of 2 will group 4 voxel together (2 in the X-direction and 2 in the Y-direction) as 1 voxel with as gray value the mean gray value of the 4 voxels. Since pixels are grouped together. the necessary amount of memory is calculated and compared with the total amount of memory (RAM). When you want to filter the noise within the images or want to speed up the segmentation functions. Save project As Allows you to save the project with another name. Reduce Images High-resolution images can contain a lot of noise and this means that a noisy 3D is obtained. use a voxel reduction. a reduction is proposed. The path of the selected folder is shown at the top. Save project Saves the Mimics project. This function groups voxels together when loading the study. every single voxel will be loaded. If more memory is needed than available. Right-click on a folder to display the following context menu. The folder will not be removed from your computer. Rename Remove To change the name of the folder To remove the folder only from the list of favorites. The maximum allowed reduction is 5. The reduce Images window (see picture) is shown when loading data sets that require more memory than available or when the preference setting “Always ask to reduce images when loading” (on the General tab page) is selected. Based on the amount of images and the pixel size. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm 2/3/2014 .File Menu Page 3 of 74 Help Opens the help pages on the Open project subject List of favorites Click on a folder to see the images within the folder. A reduction value of 1 means no reduction. the noise is filtered out and all segmentation tools work faster.

you can choose to compress it. You can choose between three different quality presets for the JPEG compression: When saving a project. STL tab and in the 3D window. When you have done a reduction on the images during loading or importing. It will appear in the Project Management. The compression algorithm used is a lossy JPEG compression. It is possible to choose between three quality presets:    High Quality – Low Compression Medium Quality – Medium compression Low Quality – High compression The higher the compression factor is. Close project Closes the Mimics project. you can also choose to keep the reduction when you are saving the project. Import STL file Loads an STL file into the project. the program will prompt you to save it. This way you can reduce the size of your projects. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.File Menu Page 4 of 74 When saving the project. If necessary. Using this option will reduce the size of the project. the smaller your files will become.htm 2/3/2014 . but the worse your image quality will be. it is possible to compress the images in the project with a lossy JPEG compression.

you will see following interface: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. The first time you use the STL Library. Mimics will ask where you want to create this library: We recommend creating a new folder on a hard disk with a lot of free space. the function is disabled if no project is opened. STL Library The STL library allows you to create a library with STL files on your hard drive that is easily accessible from Mimics. After you have selected the directory where the STL library will be located.File Menu Page 5 of 74 Note: You can only load an STL file if a project is open.htm 2/3/2014 .

Product Line and Description when viewing the properties of an STL by clicking on the fields. first close all projects and than select Import images from the File menu. you will see a list on the right of all the STL’s that are found in that directory. The wizard will start with STEP 1. If you select an STL in the tree.File Menu Page 6 of 74 The interface is divided in two parts: the left part will show a directory tree of your library. Click Next to continue the conversion. you need to browse to the folder “SCSI adaptor”. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. You can also adjust the Name. Selecting images to import The first step is to choose the source directory of the images to import. Click on the + sign in front of “SCSI adaptor” to see the list of optical drives. Import images To start the Import Images wizard. When you select one or more STL’s in the tree or in the list on the right and click the Load button. You can also create new directories or remove files via this way. all images within the directory are displayed at the right side and are immediately selected. You can click immediately on the drive or folder in the favorites column or you can browse for the drive or folder in the Windows Explorer tree. If you select a directory in the tree. When you look for images on an optical disk or tape. the selected STL’s will be loaded in Mimics. Click on the optical drive and browse to the folder with the images. These changes will be saved to a small XML file in the STL library. You can create new folders and import STL files in the library by clicking on the appropriate buttons in the STL library interface. As soon as you select the source directory. you will see the properties for that STL in the right part. The changes will be visible the next time you open the STL library in Mimics or when you click on the Refresh button.htm 2/3/2014 . You can extend the library in two ways:  You can copy STL files in the STL library folder via the Microsoft Explorer. Manufacturer.

Filename This window displays all the files in the selected Source Directory.htm 2/3/2014 . you can toggle between viewing the studies as specified in the DICOMDIR or viewing the files. This option allows you to import any type of images by providing Mimics all the image information yourself. For more details. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Right-click on a favorite folder (except for the Browse folder) to delete or rename the folder. To display the images stored on a CD (if a CD drive is available). go to the Manual import page. To display the images stored on a floppy disk (if a floppy drive is available). Each favorite folder can be dragged to another place in the list. All images are automatically selected. check the Manual import option before clicking the Next button. Browse DIA Floppy CD To browse through the folders on your computer. To restrict the selection you can hold down   the CTRL key and left mouse button to select the images one by one the shift key and left mouse button to select the first and the last image in your selection Import Toolbar Add the selected folder to the Favorites column Select all the images/projects in the Filename window Displays a window with extra information about the images to import Rebuild the DIA database in order to display recently received images To merge 2 or more image sequences of one patient To delete images within the DIA folder When there is a DICOMDIR file available in the folder. To add a new folder as favorite you need to browse for that folder in the Windows Explorer tree and click the Add favorite button in the toolbar. To display the images received via a DICOM network (if the Dicom Input Application module is installed and licensed). Select this button to display the images in the subfoldes To dump images from a tape Manual import If Mimics does not recognize the image format.File Menu Page 7 of 74 Favorites The following folders will be listed as favorites when starting the Import images wizard for the first time.

orientation. To merge one or more sequences to one Mimics project.htm 2/3/2014 . step 3 will be skipped and you will go automatically from step 2 to the next step. This function allows you to set the Bottom and Top of a patient on the Bottom and Top of the screen.File Menu Page 8 of 74 Selecting studies to convert In this window information is shown about the studies you are going to convert. The parameters that Mimics checks for are: height. Notice that when you click the Back button. Selecting studies to open Select in this window the study you want to open in Mimics. you are able to add some more studies to the list. . type of compression. Click the Convert button to start the conversion.. image6.) about the study to convert. It is a lossy compression and changes the grayvalue of all the voxels with a grayvalue between 0 and 200 to 0 MR: this compression is typically used for the removal of noise for MR-images. pixel size. Compression There are different types of image compression to choose:    CT: this compression is typically used for the removal of background noise for CT-images. will be imported. the first sequence has a skip images setting of two. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. by selecting one of the studies (the selected study will be colored blue) and then choose how many images to skip.. Lossless: when choosing lossless compression. If one of these parameters are different. width. All studies that are selected will be converted and for those studies. a Mimics file will be made in the default working folder.. In this way you can perform a batch conversion. To unselect a study. patient information. this means that not all image parameters are equal. pixel size. If the data contained only one study.. image9. If multiple image sequences of the same patient are displayed. Merging sequences in not allowed when the patient name. Mimics splits the data set in different parts. It is a lossy compression and sets the grayvalue of all the voxels with a grayvalue between 0 and 10 to 0. Invert Table Position When this option is active. select them by using the SHIFT key and left mouse button. Study In this area you can find information (number of images. nothing is changed to the voxels of the images Note: for technical CT images it is best to use the lossless compression. study information and reconstruction center of the images. gantry tilt. This means that only image0. Note: Mimics checks for several parameters during the import of images. The differences are highlighted in bold. Skip Images You can choose to skip images during the import. You can also select which studies should be converted by changing the checkmark in the Convert column. label. pixel size or image orientation is different. In the screenshot above. click on the checkmark in front of each study. the table position will be inverted during import. and click the Merge button . image3.

Click the Close button to save the correct sign. but the sign is not. The sign of the gantry tilt can be positive or negative. If you're not sure about the correct sign.File Menu Page 9 of 74 Changing orientation and gantry tilt sign If one of the orientation parameters is unknown. The gantry tilt is the angle of the scanning plane relative to a vertical plane. a window Change orientation is displayed on top of the images. You need to fill in the missing orientation strings. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. right-click on the X and choose one of the remaining orientation characters. To do this. A decision about the correct sign has to be made by visual inspection of the images in the YZ or sagittal view. contact the radiologist.htm 2/3/2014 . When the patient has been scanned at an angle (see picture) a Gantry tilt window will pop up after the import. You can change the sign by clicking the Switch button. This means that the absolute value of the gantry tilt is known. but there is no convention for this. before you can proceed. indicated by an X.

The image will be moved up or down one position in the list.65535) represents the horizontal and vertical size of the input image(s) in pixels. In this Bmp/Tiff Import window you need to fill in some image related coordinates before a conversion can be performed. Common values are 256. 320. 512 and 1024.htm 2/3/2014 . Filenames The data you want to import can be seen here. you have to change the size of these images manually in an image-editor. Note: If Mimics displays the error message that your images are not the same size when you want to import them. Files Sorting Sorts the images numerical or alphabetical. Image Information Image size This value (0 . like Photoshop. The sort order can be changed interactively by selecting an image in the list and clicking the Up or Down arrow in the Move box. Reading Tiff and Bitmap images When you select images in Bitmap or Tiff format an extra window will be displayed on the screen after clicking Next in the first Import images Wizard window. But this change results in the loss of all your segmentation.File Menu Page 10 of 74 Note: the orientation strings can still be changed after loading the project by selecting Change Orientation from the File menu. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. The radiologist should provide this information. The gantry tilt sign cannot be changed anymore after the project is loaded.

click the Update button to update the Preview. It is advised not to use a gantry tilt. allows you to check the used parameters before conversion. interpolations and 3D representation will have an inferior quality due to the gantry tilt. This option defines the distance in mm between all image slices converted at once. The first column should list all the file names (with extension) and the second column all the corresponding table positions. This can be arranged by filling in the correct value for this parameter. a mirrored model might be the result. In between these 2 columns there need to be a TAB. This option defines the actual size of one image pixel in mm. If unknown.File Menu Page 11 of 74 Import table position from This option allows you to convert Bitmap or Tiff images with a variable slice distance. even if the distance is variable. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. You need to browse to a text file by clicking on the button with the yellow folder. By selecting this text file. Note: A correctly filled in orientation is very important. he will give you the message "Not all files could be assigned a table position". i.e. the orientation can also be changed after the conversion. first make an Excel sheet and then export from within Excel to a text document with a tab in between the 2 columns.htm 2/3/2014 . Show Preview The Show Preview button. The text file should contain 2 columns. In order to make a text file very quickly. the first table position and a slice distance parameters will become disabled. Slice distance Pixel size Gantry Tilt Exam Information Patient Name Institute Name Orientation Fill in the Name of the patient Fill in the Name of the Institute Fill in the Orientation string of the patient. Mimics will put every image on the right table position. The software always assumes that the pixels are square! This option defines the angle of the scanning plane relative to a vertical plane. Mimics will proceed and makes a Mimics project with all images on the correct table positions. except for the case in which two conversion steps are necessary. whether they are stored in one file or not. It is very important to know whether a patient has been scanned with a gantry tilt (angle different from 0) or not. First Table position This option defines the table position for the first image slice of the first input file. Always try the default value. If filled in incorrectly. Although the MIMICS software has been adapted to support data scanned with gantry tilt. When changing a parameter. a table position of 0. If you selected more files than written in the text file. In this case you have to ensure the correct distance between the images converted in the first step and the images converted in the second step. If you click OK. fill in the default XXX. After selecting this option.

the following window appears. Values can be examined image by image or can be sampled through the complete data set. Values below this user minimum will be converted to black. The contrast is immediately optimized to the values of the image(s). you will also see two vertical lines moving on the histogram. If you select only one file for doing a manual import. The user can define the sampling interval. The Contrast toolbar on the bottom allows you to change the contrast. These lines indicate the interval of the values that will be taken in to account.htm 2/3/2014 . This will not only lead to an increased compression on the images but makes it also easier for the user to define proper values during the conversion operation.File Menu Page 12 of 74 The slider at the right side of the image makes it possible to scroll through the different images. By moving the contrast sliders. values above the user maximum will be converted to white. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. With this window you can import several images that are grouped in one file. Manual import When selecting the Manual import option in the Import Images wizard and clicking the Next button. you will see another window.

the orientation can also be changed after the conversion. CT3.. general structure is mostly a header with general information at the beginning of the file.. CT2.. CT101. This header size is calculated automatically by Mimics. The sort order can be changed interactively by selecting an image in the list (e.File Menu Page 13 of 74 As you can see. Multiple Files Sorting The multiple files sorting tab is only active when more than one file is selected and allows sorting the images numerical or alphabetical. Example numerical sorting CT0.. CT10. followed with an image and then between every two images a short description of each slice. The default value is 1. Only active when one file is selected. . CT12. fill in the default XXX. CT11.XP) and clicking the Up or Down arrow in the Move box. a mirrored model might be file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.1) therefore : header size = file size . Exam Information Patient Name Institute Name Slices Orientation Fill in the Name of the patient Fill in the Name of the Institute Indicate the type of slices: axial.1) Only active when only one file is selected : Number of images per file Inter-image header Size This value represents the number of image slices available within one file.CT9. This option represents the number of bytes to be skipped between every two images read from the same file.(number of images in one file * horizontal size * vertical size * number of bytes used by one pixel) inter image header size * (number of images in one file . CT1. CT100. CT4.g.. sagittal or coronal. If unknown. alphabetical sorting CT0. File Structure File Size File header Size This field gives the file size. CT1. Note: A correctly filled in orientation is very important.htm 2/3/2014 . CT5. Fill in the Orientation string of the patient. PUMP8. When a file contains more then one image. This value represents the position (number of bytes) of the first image pixel. CT10. .. A way to calculate this value : file size = header size + (number of images in one file * horizontal size * vertical size * number of bytes used by one pixel) + inter image header size * (number of images in one file .. The image will be moved up or down one position in the list. If filled in incorrectly. you can adjust the value manually. . the only difference with the regular manual import window is that you can define how many images are grouped in the file and what the header size is between each image. If needed.

Always try US first. The next table shows all possible values : Name byte unsigned byte short unsigned short long unsigned long float NR. This option defines the actual size of one image pixel in mm. The software always assumes that the pixels are square. Image Information Horizontal and Vertical image size Import table position from This value (0 .htm 2/3/2014 .e. Byte swapping This value represents to the storage format of values in the input files. You need to browse to a text file by clicking on the button with the yellow folder. If it fails. Mimics will proceed and makes a Mimics project with all images on the correct table positions. i. There are two common ways of storing values on different computer systems (and therefore also in binary files) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. In between these 2 columns there need to be a TAB. Common values are 256. If the result gives a recognizable image but with the lack of soft tissue and with low intensities. try the other pixel formats. even if the distance is variable. The default value therefore is US. After selecting this option. he will give you the message "Not all files could be assigned a table position". Slice distance Pixel size Gantry Tilt This option defines the distance in mm between all image slices converted at once. whether they are stored in one file or not. 512 and 1024. 320. By selecting this text file. This option allows you to convert Bitmap or Tiff images with a variable slice distance. first make an Excel sheet and then export from within Excel to a text document with a tab in between the 2 columns. 2 milj. use the S parameter together with an add value of 1024. If you click OK. The text file should contain 2 columns. 4 0 4 milj 4 non integer values The most common pixel formats are US and S. First Table position This option defines the table position for the first image slice of the first input file. a table position of 0. Always try the default value. Pixel properties Pixel type This option is a string representing the different formats available for storing pixel values. The first column should list all the file names (with extension) and the second column all the corresponding table positions. If you selected more files than written in the text file.File Menu Page 14 of 74 the result. In this case you have to ensure the correct distance between the images converted in the first step and the images converted in the second step.65535) represents the horizontal and vertical size of the input image(s) in pixels. In order to make a text file very quickly. This can be arranged by filling in the correct value for this parameter. of bytes Range of values 1 -128 127 1 0 255 2 -32768 32767 2 0 65535 4 -2 milj. This option defines the angle of the scanning plane relative to a vertical plane (see figure). Mimics will put every image on the right table position. the first table position and a slice distance parameters will become disabled. except for the case in which two conversion steps are necessary. or ask your client which pixel format they are using.

The user can define the sampling interval. you will also see two vertical lines moving on the histogram.) Another possibility is that the range of pixels will be scaled. When the Templates Tab is pressed. old ones can be copied (Save As . New templates can be created. Always try the default value 0 to 4095 together with a US pixel type. to store an ushort value. These lines indicate the interval of the values that will be taken in to account. (Which are not common. you can easily try out both. UL or F. deleted or used. When changing a parameter. Low byte first (DOS): storage order of multiple bytes to represent large values is from Least Significant Byte to Most Significant Byte. Values can be examined image by image or can be sampled through the complete data set. the Templates window appears. If in this case a lot of information is missing in the images (e. 2 bytes are needed. The Contrast toolbar on the bottom allows you to change the contrast.File Menu Page 15 of 74 High byte first (SGI): storage order of multiple bytes to represent large values is from Most Significant Byte to Least Significant Byte. Minimum Image value Maximum Image value These values represent the range of pixel values (intensity) to be projected in the range of 0 to 4095. allows you to check the used parameters before conversion. but some use negative values as well as positive values. This is necessary only for images with pixel types L. Pixel size and all other exam information are case dependent and not depending on the scanner. The slider at the right side of the image makes it possible to scroll through the different images. all soft tissue) and the default threshold value in MIMICS has no sense. one representing the most significant part. Show Preview The Show Preview button. then use the S pixel type together with the correct min and max value. As there are only two possible values. Most probably. The contrast is immediately optimized to the values of the image(s). Values below this user minimum will be file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.). The ordering of these two bytes can be Most significant first as well as Least significant first. If with one value.)- Templates A template containing all parameters can be stored for future use. click the Update button to update the Preview. (This is most often a value of –1024 and 1024.htm 2/3/2014 . Please keep in mind that parameters such as Slice Distance. change the option to the other value. In these cases you have to specify the S pixel type instead of US and enter the correct Minimum Image value and Maximum Image value to ensure that all output pixels will have positive values.. E.. By moving the contrast sliders. the output images look very noisy and have no clear visual information.g.g. your client will not be able to give you this information. All CT scanners will create images with a range of at most 4096 different values. one representing the least significant part of the value.

Curves tab and click on the button called New. You can set the size of the preview in the drop down list at the left bottom. The reslice file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. based on this curve. This can also be done by checking or un-checking the project column (2nd column) in the Image List or the images in the grid on the right. connected by an interpolated line.. The red marked images will be displayed in the project. The orientation strings within the images. You can change the current contrast to the default for CT or MR images by clicking on the appropriate bullet. Shows a preview of the images if selected. "A". Note that all the other orientation strings are completed automatically. objects etc. Change orientation If one of the orientation parameters is unknown a window "Change orientation" is displayed on top of the images. "R". measurements etc. values above the user maximum will be converted to white. The radiologist should provide these orientation parameters. Posterior. The cursor shape changes to a hand and if you right-click. Adds or removes images from the project. "L". When marked all unselected images will be removed from the project.. The orientations that Mimics needs to know are the Left-Right. Anterior. These minimum and maximum contrast values can be changed in the adjust grayscale toolbar.File Menu Page 16 of 74 converted to black. Displays the current minimum and maximum contrast values for displaying the images. The parallel and cross-sectional images are constructed. The orientation parameters are necessary to display the images correctly in Mimics. the Anterior-Posterior and the Top-Bottom orientation. Move the mouse cursor to an X in the sagittal or coronal image. Online reslice Using this function you can reslice your project drawing a curve on the axial images. You will see immediately the result in the images. every 2 images with the skip images setting at the bottom of the window.htm 2/3/2014 . This will not only lead to an increased compression on the images but makes it also easier for the user to define proper values during the conversion operation. Select File > Online Reslice from the menu or go to Project Management. when you organize your images. You can easily select e. "P". Organize images In the organize images interface you can choose which images in your Mimics project should be visible and used while working with Mimics. measurements. but sometimes this information is incomplete (in this case there is a red X instead of a string in the orientation windows). a menu appears with all possible orientation strings. Here you can select/unselect the images. respectively stand for Left. The curve consists of a series of points. when you change the orientation of your project. Note: Please be advised that you can loose existing segmentations. "T" and "B". Preview Contrast Delete Unselected images Add/Remove Note: Please be advised that you can lose existing segmentations. Right. Image List List of images.g. Top and Bottom. In this last step you need to verify the orientation before you can proceed. This action can not be undone.

The reslice curves toolbox Select a reslice curve Select the cursor tool and click on a reslice curve to select it. Reslice Curve Dialog Click on this button to visualize the Curves tab in the Project Management X-Ray image A yellow border surrounds the X-ray image or parallel view. click on this button . The selected point will be colored green. The points of a selected reslice curve are in white. Its thickness can be set in the Reformatting tab of the Preference Settings (choose Options > Preferences > Reformatting from the menu bar). Create a reslice curve Creates a reslice curve. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Click with the left mouse button to add a point. next to the parallel view.htm 2/3/2014 . Click several times with the left mouse button on the axial image to create a reslice curve. To display the x-ray view. The points of a non-selected reslice curve have the same colour as the lines of the reslice curve. To return to the parallel view. Add a point to a reslice curve Click on the Add point to reslice curve button to add a point in the middle of the selected line. Click on the remove point from reslice curve button to delete the point. Remove a point from a reslice curve Click on the point of the reslice curve you want to delete. the cursor will change into a pencil. click on this button: . Double click with the left mouse button or click with the right mouse button to finish the reslice curve. The action you do is always performed on the selected reslice curve. Note: STLs are only visible in the parallel images when a straight online reslice curve is drawn. When you hover the mouse above the reslice curve. Delete reslice curve Select the reslice curve you want to delete and click on the Delete reslice curve button.File Menu Page 17 of 74 curves toolbox will appear on the screen with the second button already selected. The cursor will change to a pencil.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. you will see the original view again. By clicking with the unzoom tool on the enlarged cross-sectional image. The bounding box of the new image volume will be shown on the 2D images and in the 3D view. Original View Zoomed cross-sectional image Reslice Project You can reslice a project by going to the File menu and then choose the Reslice Project button.File Menu Page 18 of 74 Zooming in Reslice Layout When you left-click once when zooming on a cross-sectional image. There is an easy to use interface available. The mouse icon will change to a pen and you will be able to draw a straight line in any of the 2D views by clicking once with the left mouse button to indicate the starting point. that image gets enlarged. click again with your left mouse button on the ending point of the line.htm 2/3/2014 . To finish drawing the line. Following window will appear: Projects can be resliced according to a straight line in any direction. The reslice line can easily be drawn in the 2D or 3D views by clicking on the Draw Line button. This will create a new Mimics project on your hard drive.

The file with the transformation matrix will be saved in the folder of the original project. you can still adjust the end points of the reslice line. we create a new Mimics project for only the femur. Following window will appear: The outlines of a box will appear on your 2D views and 3D view. Several predefined orientations can be chosen in the orientation dropdown. When reslicing a project. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. You can also rotate the project that will be resliced around the reslice line by adjusting the rotation angle. Mimics will also write out the transformation matrix that was applied during the reslicing. a new Mimics project will be created for only that part of the dataset in the box. When you apply the cropping. In the following example.File Menu Page 19 of 74 The coordinates of the beginning and end point of the reslice line can be adjusted in the edit fields.htm 2/3/2014 . The box can be adjusted by dragging the borders of the box in the 2D views or by adjusting the box properties in the crop interface. height and slice distance can be specified and you immediately get information about the number of slices that will be in the resliced project. Since the cropped project will contain smaller slices. the speed of Mimics will be increased while working on the project. This way it is possible to create a small project for only the structure you are interested in. starting from a dataset that contains the hip. Crop Project You can crop a project by going to the File menu and then choose the Crop Project button. After drawing. Image width.

File Menu Page 20 of 74 When cropping a project. the clinician name and some comments. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Mimics will write out the transformation matrix that was applied during the cropping. With the copy button you can copy all the project information in order to paste it in a document. The file with the transformation matrix will be saved in the folder of the original project. Export anonymous project This function will save a copy of the project without any patient related information.htm 2/3/2014 . After clicking the edit button you can add or change the dentist name. Project information This window displays the most important project information.

htm 2/3/2014 . measurements. To the printer: select Printer to print the image To clipboard: copies the image to the clipboard allowing you to paste it into another application 2. first before creating the image or print. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. A default name will be proposed (patient name + view) and the default folder will be the folder where the project is stored. so you will have to prepare your screen with rulers. You can select 2 destinations: 1. The image or the print will show you exactly the same information that is on the screen. . you will immediately see a preview on the right. . . You can browse to a new folder by using the yellow button on the right.File Menu Page 21 of 74 Save/print screenshot After selecting the image type on the left of the screen. To a file: Select Filename in the Destination frame to save the image as a BMP or JPEG file. 3.

after an Online Reslice. the cross-sections and parallel images. coronal. sagittal images and. Properties Resolution White background Resolution of the images Option to print a white background file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.File Menu Page 22 of 74 Printing Allows you to print a standard report showing a General Information page. the axial.htm 2/3/2014 .

You can display the next or previous page by clicking the buttons Next and Prev. For example 1. Functions Advanced Edit Info Print Setup Page Setup Print To set some advanced print options. If you prefer another setting permanently. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.File Menu Page 23 of 74 Dithering Option to print the page dithered or not (halftone) . To select the printer To define the page margins and the font. This information will be shown in the prints. Advanced Printing In this Advanced Print dialog box you can temporarily overrule some print preferences before printing.htm 2/3/2014 . To start printing Edit Info In this dialog box you are allowed to type some information concerning the study.printer dependent Navigation Display in the Print Preview a specific page of your standard report by clicking the arrow button and selecting one of the pages out of the list. You can also choose the unit: mm or inch. Open this dialog by clicking the Edit Info button in the Print window. go to Options > Preferences > Printing.3. Print Pages All pages Current page Range Print all pages Print only the page in the print preview Enter the page numbers and/or page ranges (separated by commas) for the pages that have to be printed. To add comments on the prints.5-12.

The important point is the center point of the box and not really the edges. Click once on the file name to open the study. Select the objects to print. Codonics printers.File Menu Page 24 of 74 Pages to print Objects to print Distances between images Axial image Printer info Select the pages to print. Use the force color option when you have a color-printer. To move the box. Spacing between the cross-sectional images and the parallel images in the prints. you only get black and white prints. This can happen with e.htm 2/3/2014 . Exit Will Close the Mimics application and will save if necessary. If the crosssectional spacing in the prints is not the same as in the images a message will appear about measurements that may not be visible anymore. select one of the edges and drag it with your left mouse button. The box in the axial image indicates the region of interest. but when you print a project. In this window you will find the info about the printer that you have installed. List of previously opened files A list of recently processed files is shown in the File menu or when you click on the arrow next to the folder icon in the toolbar.g. Edit Menu file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.

View Menu This menu contains the following items. Every action is added to the top of the list. The type of action is mentioned after the word "Redo" in the Edit menu. so the first one on the list is the last action performed. The type of action is mentioned after the word "Undo" in the Edit menu.File Menu Page 25 of 74 The edit menu contains the following items: You will also find the corresponding buttons in the toolbar. Redo Redo the last action you have "Undone". file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Undo Undo the last action performed.htm 2/3/2014 . Show undo list A list is displayed with all actions that have been performed.

File Menu

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You will also find the corresponding buttons in the toolbar.

Toolbars
Mimics lets you choose which toolbars are visible and which are not.

The toolbars are shown as tabbed toolbars by default. They can be undocked from the main toolbar by selecting the tab with the left mouse button and dragging it outside the toolbar.

To dock a toolbar back into the main toolbar, select the toolbar bar and drag it over the main toolbar.

Main toolbar
A Main toolbar is displayed underneath the menu. It holds the other toolbars as different tabs. If the Main toolbar is not displayed, select View > Main toolbar from the menu bar. You can remove the Main toolbar by selecting View > Main toolbar from the menu bar again. You can dock the Main toolbar along the top or allow it to float freely anywhere in the image area by dragging it into place.

Tools toolbar
A Tools toolbar can be activated by on of the tabs next to the main toolbar. If the Tools toolbar is not displayed, select View > Tools toolbar from the menu bar. You can remove the Tools toolbar by selecting View > Tools toolbar from the menu bar again. You can add the Tools toolbar as a tab to the main toolbar or allow it to float freely anywhere in the image area by dragging it into place. The Tools toolbar displays buttons that are shortcuts to the following menu commands: Measure a distance

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Measure an angle Measure a distance in the 3D view Measure an angle in the 3D view Measure the area and average density within a rectangular region Measure the area and average density within an elliptical region Add an annotation to a Mimics object Draw a profile line Show 3D histogram

Segmentation toolbar
A Segmentation toolbar can be activated by on of the tabs next to the main toolbar. If the Segmentation toolbar is not displayed, select View > Segmentation toolbar from the menu bar. You can remove the Segmentation toolbar by selecting View > Segmentation toolbar from the menu bar again. You can dock the Segmentation toolbar in the main toolbar or you can allow it to float freely anywhere in the image area by dragging it into place. The Segmentation toolbar displays buttons that are shortcuts to the following menu commands: Thresholding Region Growing Dynamic Region Growing Morphology Operations Boolean Operations Cavity Fill Edit Masks Multiple Slice Edit Crop Mask 3D Mask Editing Calculate Polylines Update Polylines Calculate 3D Label Cavity Fill from Polylines Calculate Polylines from 3D Calculate Mask from 3D

Navigation toolbar
A Navigation toolbar can be activated by on of the tabs next to the main toolbar. If the Navigation toolbar is not displayed, select View > Navigation toolbar from the menu bar. You can remove the Navigation toolbar by selecting View > Navigation toolbar from the menu bar again. You can dock the Navigation toolbar as a tab onto the main toolbar or allow it to float freely anywhere in the image area by dragging it into place.

You can navigate to a certain position in the image dataset by filling in coordinates in the edit boxes for the Axial, Coronal and Sagittal slice position and by clicking on Apply.

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If you change the position of the images by scrolling through the images or by doing a one-click-navigation, the slice positions in the navigation toolbar will update automatically.

Status bar
A status bar is displayed along the bottom of the screen. If the status bar is not displayed, select View > Status Bar from the menu bar. You can remove the status bar by selecting View > Status Bar from the menu bar again. The status bar displays the following useful information:    tips that describe actions taken by tools and menu commands current gray scale value or Hounsfield unit in the voxel currently pointed at by the cursor current cursor position in 3D coordinate system

Project Management
The project Management gives you an overview of the different objects. If the Project Management is not displayed, select view > Project Management from the menu bar. You can find more information about the separate tabs in the in the Project Management chapter in the General Information part.

Project Management tabs
You can Show/Hide each tab in the Project Management

Interpolated images
This function will allow you to toggle between an interpolated view of the reslices in XZ and YZ direction

Interpolated Images off

Interpolated Images on

Note: This function will only interpolate the grey value images, the mask will remain the same. Editing on the mask on interpolated images is possible.

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Show/Hide
The following menu is shown:

Show Masks Hide Masks Show measurements Hide measurements Show CAD objects Hide CAD objects Show polylines Hide polylines Show annotations Hide annotations

make all masks visible when they are invisible make all masks invisible when they are visible make all measurements visible when they are invisible make all measurements invisible when they are visible make all CAD objects visible when they are invisible make all CAD objects invisible when they are visible make all polylines visible when they are invisible make all polylines invisible when they are visible Make all annotations visible when they are invisible make all annotations invisible when they are visible

Pan view
Every image and 3D object can be panned or moved. When you select the pan function, the cursor will change to a cross-shaped double arrow. There are different ways to select the pan function:       hold down the SHIFT key, right-drag your mouse button right-click in an image or in the 3D view and select Pan View from the context menu click on the Pan View button in the toolbar hold down the SHIFT key in combination with the arrows-keys for precise rotation Hold down the SHIFT key in combination with Home / End for quick Left / Right panning select View > Pan View from the menu bar

Rotate view
The rotate function is only available on a 3D object. There are different ways to select the rotate function:        right-drag with your mouse button use the arrows-keys for precise rotation use Home / End to rotate 10 degrees Left / Right use Page Up / Page Down to rotate 10 degrees Up / Down right-click in the 3D view and select Rotate View from the context menu click on the Rotate View button in the toolbar select View > Rotate View from the menu bar

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Zoom
Allows to Zoom in at a user defined rectangle. Click on the left mouse button to indicate a corner of the zoom rectangle, drag and release to indicate the opposite corner. Can be used on every image. There are different ways to select the zoom function:       hold down the CTRL key, right-drag your mouse button hold down the CTRL key in combination with the up / down arrow keys hold down the CTRL key in combination with the Page Up / Page Down key right-click in an image or in the 3D view and select Zoom from the context menu click on the Zoom button in the toolbar select View > Zoom from the menu bar

Note: The behaviour of zooming is different in Reslice Layout.

Unzoom
Changes the display scale to show the whole image. You need to select the function first and then indicate the view on which you want to apply the function.

Zoom to full screen
Allows you to display a view on the whole screen. Click on the Zoom to full screen button and the cursor will change to a magnifying glass. Then click on an image. To return to a normal view, click again on the Zoom to full screen button.

Zoom to full screen on axial view

When you hover with the mouse over a view and press the spacebar the view is also put to full screen. To unzoom press the spacebar again.

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3D Background color
Click View | 3D Background Color from the menu bar to select another background color for the 3D image.

To set a default color, click Options > Preferences > Color from the menu bar.

Toggle gray scale
You can quickly toggle between the last two gray scales you selected in one of several ways: select View > Toggle Gray Scale from the Menu bar or press the Toggle Gray Scale button on the Main toolbar. The current gray scale's description, level and width will be displayed on the status bar.

Pseudo Colors
Mimics provides you with several color scales that can be helpful in viewing the image data. One gray scale and three pseudo-color scales are provided. The pseudo color scales vary the hue (color) and luminance (brightness) within the images. Use color scales to enhance small differences in the soft tissue or the bone. Unlike the gray scale, the pseudo-color scales are non-linear. The pseudo-color scales can be used for instance to examine the porosity in materials. You can change the scale to one of the pseudo-color scales by selecting View | Pseudo Color from the menu bar and selecting one of the three color scales from the cascading menu. To revert back to a gray scale, select Gray from the cascading menu.

Gray
This is the default gray scale.

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Full Spectrum
The Full Spectrum color scale varies within the standard, continuous range of hues from orange to yellow to green to blue to red. In order to make air black and bone white, it also varies in luminance from dark (black) to light (white).

Sawtooth
The Sawtooth color scale places five discrete hues next to each other. In order to emphasize differences between tissues of very nearly the same tissue density, the hues are very different: orange, green, red, blue and yellow. Within each hue, the luminance varies from dark to light.

Triangle
The Triangle color scale places the same five discrete hues next to each other. But, within each hue (except for yellow, which varies from dark to light), the luminance varies from dark to light back to dark again.

Masks Shades
Mimics allows you to change the shades and transparency of the mask. The different settings are explained below: Semi All visible masks will be displayed. Only the active mask

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coronal and sagittal view in case of 3-panes setting and includes also the 3D view in case of 4 panes. In case of 3-panes setting. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Full All visible masks will be displayed and all masks will be transparent.File Menu Page 33 of 74 will be transparent. Image layout The Image Layout is the default layout. Example: Binary All masks are displayed in binary. the surrounding background is displayed in black. Example: Layouts The Layouts list let you easily switch between different layouts.htm 2/3/2014 . toggling the 3D view will replace the sagittal view. All gray shades from the surrounding tissues remain visible. For more information on how to change between 3-panes and 4-panes setting please look at the Visualization Preferences page. It shows the axial. All gray shades from the surrounding tissues remain visible. the surroundings are displayed in black. Example: Active Only the visible masks are displayed. Only the active mask is transparent. Click on the image below to see more information about the different layouts.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Reslice layout This layout is only enabled after an online reslice. there is a 3D toolbar and each 3D can be manipulated separately. In case of 3-panes setting. In each 3D view. cross-sectional and parallel view.File Menu Page 34 of 74 3D layout The 3D layout shows an axial view and 2 3D views in the 3-panes setting and 3 3D views in the 4-panes setting. It shows the axial.htm 2/3/2014 . toggling the 3D view will replace your axial view.

You can find more information about changing the orientation on the Change Orientation help page. Scanogram. Topogram. or Surview depending on the CT manufacturer) is a lateral X-ray-like view of the patient. the Toggle 3D button is not present. Left clicking in the alignment image allows you to navigate in all images. when using a wrong orientation for a project. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. The H and F markers show you the direction toward the patient’s head and feet.File Menu Page 35 of 74 Toggle 3D Window To view the 3D pane in the Mimics work area in 3-panes setting. Click the Options button to adjust 3D generation parameters to your needs. The 3D objects list dialog will be shown. Notice the red vertical line. in which case you see all image views and a 3D view. The 3D is automatically shown on your screen after calculation. select View > Alignment Image from the menu bar. ScoutView. The alignment image is surrounded by a frame border. you can calculate a 3D by selecting this button in the Segmentation toolbar: . Inspect the alignment image to check that your patient was positioned correctly for the CT scan. You can also work in 4-panes setting. Toggle 3D If you have not yet created a 3D. It references the exact location of the axial image. Then click the Calculate button to start calculating the 3D. The sagittal view will be replaced with the 3D view and a 3D toolbar. To remove the alignment image.htm 2/3/2014 . Alignment image You can view the alignment image by selecting View > Alignment Image from the menu bar or by clicking the Alignment Image button on the Main Toolbar. You can move the alignment image anywhere on the screen by dragging its title bar. Pilot. click on the 3D button on the Main Toolbar. The dashed red lines reference the first and last axial images and show the extent of the area that was scanned. Note: Be aware that the Alignment Image will display incorrect information. listing all 3D objects. click the Alignment Image button on the Main Toolbar. The alignment image (also called a Localizer. or click its Close icon. In that case.

A measurement will be shown together with its length (expressed in mm). Measure distance This tool allows you to measure distances within the images. right-click on the measurement. Click once the left mouse button to set the first point.File Menu Page 36 of 74 Tools Menu The Tools menu contains the following items: You will also find the corresponding buttons in the toolbar.htm 2/3/2014 . Select the measurement icon from the tools toolbar or select Tools > Measure distance from the menu. To show its context menu. The cursor will change in a measuring rule. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Fine adjustments can be made to the measurement by dragging either end to a new location. Click again to fix the other end of the measurement.

Select the 3D angle icon from the tools toolbar or select Tools > Measure 3D angle from the menu. Fine adjustments can be made to the measurement by dragging either end to a new location.htm 2/3/2014 . To show its context menu. Click three points with the left mouse button to define the angle. right-click on the measurement. Delete Hide Delete the measurement Hide the measurement Measure 3D angle This tool allows you to measure angles in the 3D window. The angle is expressed in degrees and shown on the screen. You can measure distances on the same object or between different objects. To show its context menu. Click three points with the left mouse button to define the angle. Fine adjustments can be made to the angle by dragging the center point or one of the ends to a new location. right-click on the angle. The cursor will change to a measuring instrument. Fine adjustments can be made to the angle by dragging the center point or one of the ends to a new location. While you move over the 3D you will notice that a star will follow the surface of the 3D object. The cursor will change to a measuring instrument. Both angle measurements between different 3D objects or measurements on the same object are possible. Select the angle icon from the tools toolbar or select Tools > Measure angle from the menu. Delete Hide Delete the angle Hide the angle Measure 3D distance This tool allows you to measure distances in the 3D view. Click once the left mouse button on a 3D object in the 3D view to set the first point. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. The cursor will change in a measuring rule. Select the 3D measurement icon from the tools toolbar or select Tools > Measure 3D distance from the menu.File Menu Page 37 of 74 Delete Hide Delete the measurement Hide the measurement Measure angle This tool allows you to measure angles within the CT images and the alignment image. A measurement will be shown together with its length (expressed in mm). The angle is expressed in degrees and shown on the screen. Click again to fix the other end of the measurement.

Move the rectangle to the image you want to measure. Click to drop the rectangle on the image. Or. right-click on the angle. When you release the mouse button. When you scroll through the images. right-click on the rectangle. To move the ellipse. the density (Hounsfield Units or Gray Values) and the standard deviation of the density (Hounsfield Units or Gray Values) within the elliptical region is displayed. The rectangle expands and contracts as you move the mouse.htm 2/3/2014 . To show its context menu. You can adjust the size and shape of the ellipse by dragging one of the four markers on the ellipse when the cursor changes to a double arrow. Delete Hide Delete the rectangle Hide the rectangle Measure density in ellipse This tool allows you to measure the area and average density. Move the ellipse to the image you want to measure. To move the rectangle. Delete Hide Delete the angle Hide the angle Measure density in rectangle This tool allows you to measure the area and average density within a rectangular region. Click to drop the ellipse on the image. Select the ellipse icon from the tools toolbar or select Tools > Measure density in ellipse from the menu. the measurements are updated. drag the left mouse button to drop the ellipse and change its size in one step. The measurement data is recalculated when you release the mouse button.File Menu Page 38 of 74 To show its context menu. place the cursor on a non-marker portion of the yellow border (the cursor changes in a hand) and drag it. Or. within an elliptical region. Information appears about the area (mm²). When you scroll through the images. You can adjust the size of the rectangle by dragging a border or corner when the cursor changes to a white double arrow. Release the mouse button when you are satisfied with the size of the rectangle. the area (mm²). drag with the left mouse button to drop the box and change its size in one step. the mean density (Hounsfield Units or Gray Values) and the standard deviation of the density (Hounsfield Units or Gray Values) within the rectangle. The ellipse expands and contracts as you move the mouse. the measurements are updated. the new measurement data is displayed. When you release the mouse button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. place the cursor on a yellow border (the cursor changes to a hand) and drag it. Select the rectangle icon from the tools toolbar or select Tools > Measure density in rectangle from the menu.

Selected the annotation tool and left click your mouse. To show the annotation context menu. When you double-click the text comment. Delete Hide Delete the ellipse Hide the ellipse Add Text Annotations You can add text comments using the annotation tool . right-click on the annotation. the Annotation Properties dialog will pop up.File Menu Page 39 of 74 To show its context menu. Delete Hide Properties Annotation List Deletes the text annotation Hides the text annotation Opens annotation properties dialog Brings the annotation tab in the project file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. 2D and 3D views. right-click on the ellipse. Arrow Style Text Rotation Text alignment Text Style of the line ending Direction of the text Alignment of the test Comments that will be shown in the project Note: When you add a long text as comment. you can edit it. The full text is shown when you hover over the annotation. You can now add your comments in the text field.htm 2/3/2014 . it will be visualized as three little dots. You can indicate structures on the images or on the objects in both. Select the annotation tool and indicate the structure on which you want to comment.

List of profile lines Profile Visible Profile name of the profile line.htm 2/3/2014 . Options Scale to fit Grid X-axis Grid Y-axis Allows you to see the vertical axis with all Hounsfield values or only the values lower than the maximum value along the profile line. Figure In the figure you can see the intensities for each point along the created profile line. The Profile dialog graph will be displayed: . Click on its name to change it (similar as in Windows Explorer). click the left mouse button to indicate the starting point of the profile line. Measuring There are three measurement methods: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. move the mouse to the end position of the line and click again. To draw this line.File Menu Page 40 of 74 management to the front Profile line Visualizes an intensity profile of the HU or Gray Values along a user defined line. this dialog box will be closed/ opened and the threshold will be applied in your images. To show or hide the horizontal grid lines. Functions on profile lines Color Delete End/ Start Thresholding Allows you to change the color of the selected profile lines. Shows by means of glasses if the profile line is visible or invisible in the images. By Clicking this button. The minimum and maximum threshold you want to apply can be changed by moving the horizontal lines. Deletes the selected profile lines. Left-click on the glasses to toggle between visible/invisible. To show or hide the vertical grid lines.

File Menu Page 41 of 74 4 point method (suggested for technical parts): The user will see four full lines numbered from 1 to 4. The “T” function in above expression is the percentage of threshold difference. The X-axis lists the HU or Grayvalues. The software calculates the intersection point of the vertical lines with the profile line: four points are calculated. Most of the time this is about 50%.htm 2/3/2014 . The Y-range can be logarithmic or decimal. each with a different color. along the Y-axis the number of pixels that have this value. The histogram function can be saved as a text file which can be easily imported in other programs. They are also listed in the Measure tab page of the project management. The range of this axis can be user defined or automatic (all values). The corresponding HU values can be read by following the full horizontal lines. The dashed white lines indicate this point. These four average values will than take over the role of the 4 points as described in the 4 point method. The full lines represent the input. For each interval the average value is calculated. The distance between the lines is displayed in mm. Segmentation Menu This menu contains the following items: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. On each side of the peak. Threshold method (suggested for medical images) Start the thresholding and drag the threshold line to the right position. you will also see two horizontal lines (yellow and white). To activate the changing of these settings. In case you choose the 4 point method or 4 interval method. resulting in a non-optimal view of the rest of the histogram. Like this you can always refer to the measurements made and pop-up exactly the same profile line as initially created. They indicate the position of the threshold value following the percentage filled out in the dialog box. while the threshold method is suggested for medical applications. This point is indicated by the dashed yellow lines. Note: The Grayvalue 0 (-1024 HU) is not included in the histogram. The distance between P1 and P2 is the requested dimension. The 4 point method and the 4 interval method are suggested for technical CT images. 3D Histogram The 3D Histogram is the histogram of the complete data set. The measurements are shown in the images and are saved to the project. a point is calculated as follows: P1 is at the position of the profile line where the HU value equals “T(gvalue2-gvalue1)+gvalue1” and lies between line1 and line2 on the horizontal axis. the user will indicate 4 intervals. The yellow and white dotted lines will move to the intersection between the profile line and the threshold line. P2 is calculated in a similar way but with lines 3 and 4 as parameters. the number of pixels for that value is much higher than for other values. 4 interval method (suggested for technical parts): Instead of indicating 4 points. Click on the End Thresholding button. since for most data sets. you need to click on the Update button.

With a Profile Line To use a profile line for thresholding. The threshold value will be displayed in the threshold toolbar and the segmentation area is changed accordingly. Note: The upper and lower threshold limit is limited to the maximum and minimum intensity in the project. Now you can use the measurements made with the profile line to determine the lower and upper threshold values. or based on a lower and a higher threshold. The predefined threshold allows you to quickly select a threshold for a specific tissue type.htm 2/3/2014 . With the two sliders a minimal and a maximal threshold can be set. The object can be defined based on one lower threshold. click the left mouse button again to determine the end point of this line. a threshold value can be filled in or the value can be increased or decreased using the up-down controls (ideal for fine tuning the threshold). Then. In the latter case. When Start Thresholding is enabled on the Profile Line dialog box. These lines represent the lower and upper threshold values. Thresholding There are two ways of thresholding: With the thresholding toolbar Set the threshold of the active mask. Thresholding is used to create a first definition of the segmentation object. click the left mouse button to indicate the starting point of the profile line. The threshold value can be changed by moving the sliders in the thresholding toolbar with real time visual feedback. click Enter. you can easily change the lower and upper threshold values by grabbing and moving the green lines. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Then select the profile line button from the tools toolbar. the pixel value must be in between both threshold values to be part of the segmentation object. the segmentation object will contain all pixels in the images with a value higher than or equal to the threshold value.To accept these values. You can set or change the active mask in the Masks tab of the project management. To draw the line. first select Thresholding button from the tools toolbar or select Thresholding from the Segmentation Menu.File Menu Page 42 of 74 You will also find the corresponding buttons in the toolbar. (Mostly only the minimal value needs to be set) In the Min and Max box. In the former case. press the Apply button. The threshold can still be adapted to your needs. To use the threshold.

Target The new mask that will be created or if you select an existing mask.  If you make a second mouse click. When the check "Leave Original mask" is marked. Source and target masks are set here.. all selected information will be removed from the target mask and placed in the source mask (compare it to cut and paste). Mimics will take into account the file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm 2/3/2014 . in CT images.. Mimics starts comparing the gray values of the neighboring pixels. The operation can be performed on one single slice (multiple layer is Off) or in 3D on all slices (Multiple layer is On): to do this. All points in the current segmentation object that are connected to the marked point will be moved to the target mask. If two existing masks are chosen in the source and target box. turn Multiple Layer On or Off in the Region Growing Properties toolbar. in which case the selected region will be added to this object. When it is turned off. all selected information will be copied and pasted in the new mask. The creation of this new mask starts when you select a pixel. click the left mouse button (cross shaped) on one point of the object of interest (which has to be part of the current segmentation object.). nerves. above rule will also be applied on the gray value of the selected pixel. . Dynamic Region Growing The dynamic region growing tool allows you to segment an object based on the connectivity of gray values in a certain gray value range. |î -i | < d with  î the average gray value i the new gray value  d the deviation. The Dynamic Region Growing function is the only operation where you don’t have to threshold. It allows an easy segmentation of blood vessels. The target mask can be a New mask or an existing object.File Menu Page 43 of 74 You can find more information about profile lines on the Profile Line help page. A threshold value will be set automatically. Region Growing The region growing tool provides the capacity to split the segmentation into separate objects. the double arrow can be used to switch source and target. After entering the appropriate values. The pixels with gray values that obey the following rule will be added to the new mask. the minimum and maximum value of the created mask will serve as threshold values.

htm 2/3/2014 . making it possible to instantly see what the result of a different Deviation would be. Mimics will look to the same XY coordinates of the selected point in the following slices.0 the complete grayvalue range of 12 bits (0-4095) is used so the deviation can be better fine-tuned.3 to get the same results. In-slice distance is be the distance in the plane of the original slices. Mimics will look in the complete data set. 6-connectivity will look at the neighboring pixels in 3D 8-connectivity will only look at the neighboring pixels in the plane. When auto-update is enabled. you can adjust the deviation after indicating the source of the Dynamic Region Grow. When "multiple layer" is marked. Mimics will look to the same XY coordinates of the selected point in the following slices. The maximum distance allows to limit the region wherein Mimics will search for the pixels (the endresult can thus be spherical). Example: Selection of the alveolar nerve with one mouse click: 2D 3D Morphology Operations file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Note: The deviation parameter in previous versions of Mimics was expressed with 1 byte (0-255). When this is marked. while from Mimics 8.connectivity 26-connectivity 4-connectivity will only look at the neighboring pixels in the plane.File Menu Page 44 of 74 Auto-Update Multiple Layer 4-connectivity 6-connectivity 8-connectivity 26-connectivity gray values of the pixels that are already in this mask. Deviation Distance 26-connectivity will look at the neighboring pixels in 3D. the function will only be applied on the single slice. This means that you have to use a deviation that is much higher than in Mimics 7. Inter-slice distance is be the distance perpendicular to the original slices. When "multiple layer" is marked. 4-connectivity 6-connectivity 8. A value of zero will look in the complete data set. Is the deviation parameter in above rule. When it is unmarked.

Dilate: dilate will add pixels from the edges. low mask B)) higher threshold = min (high mask A. Small edges will be removed or opened. :   Subtraction (Minus): Threshold value = Threshold value mask A Intersection : lower threshold = max (low mask A. is the amount of pixels you will take/add in one operation 8. However. This is to prevent that you will have an endresult that is larger/smaller than wanted. Source Operation The Source mask is the mask that will be altered. Close: will perform first a dilation. to take effect. immediately followed by a dilation. the result will be copied in the target mask. The different morphology operations are:     Erode Dilate Open Close All these functions will take or add pixels from the source mask. high mask B)) Union : lower threshold = min (low mask A.htm 2/3/2014 . Boolean Operations The Boolean operations allow you to make all different kinds of combinations based on two masks. You can limit the effect of dilation to another mask. immediately followed by an erosion. click the Apply button. Erode: erode will take pixels from the edges. low mask B)) higher threshold = max (high mask A. high mask B))  Example: Separation of a knee joint file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. You can limit the effect of an operation to another mask. The lower and upper threshold boundaries of the target mask will be taken over from the source mask After entering the appropriate values. After entering the appropriate masks and operation. This is to prevent that you will have an end-result that is larger than wanted.connectivity 26-connectivity 8-connectivity will only look at the neighboring pixels in the plane. click the Apply button. Open: will perform first an erosion. The threshold limits of the resulting mask will be updated according to the values of the masks A and B and the operation applied. the slice distance must be equal or less than the size defined by the number of pixels (pixelsize * number of pixels).File Menu Page 45 of 74 Morphology Operations will perform actions on the 'form' of a mask. This can be used to restore the effect of the erosion. Target Limited to : Number of pixels 8-connectivity 26-connectivity The new mask that will be created. It is a very useful tool to reduce the work that needs to be done when separating two joints. Erode followed by a region grow can separate parts. (The operation is performed on the complete dataset) 26-connectivity will look at the neighboring pixels in 3D. Small cavities will be closed.

htm 2/3/2014 .g. Therefore. The result is shown in the cyan mask. when you move the mouse now. To use the Lasso tool: select Lasso as Type. or restore the image with a certain threshold value indicated below. it is best to take a new mask to fill the cavity in. erase. the size will change. Size of the edit cursor (can be different if the Same Width and Height check box is switched off). The drawing cursor can be a rectangle or a circle (ellipse) and can have different sizes. Below the following bar appears: Type Shape of the edit cursor: square (rectangle). Please save your project first before performing the Cavity Fill. Below is a trick to fill a lot of internal holes at once: Edit Masks All manual editing functions are performed on the active mask. You can draw. So some erasing is necessary. then draw with your mouse on a slice while pressing the left mouse button. release the left mouse button.File Menu Page 46 of 74 The image with the green mask is the starting situation. To end the drawing. or you can use the lasso tool to draw a shape. As you see the tibia and femur are connected with each other. Select the cavity to fill by a click of the left mouse button (bucket shaped). Now you can subtract the purple mask with the first structure from the cyan mask that contains both structures and you immediately have the second structure (red mask). Then region grow it e. The Cavity Fill function might lead to surprising results when there is a "gap" to the surrounding area. Source and target masks are set here. to the purple mask. Width/Height file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. The size can be adjusted interactively by keeping the CTRL button and the left mouse button down. circle (ellipse) or the Lasso tool. The multiple layer check box indicates if you will fill in 3D or just in 2D. Cavity Fill Fills internal gaps of the selected mask and places this in a new mask. You only have to edit one part.

You can then click with your left mouse button on the point you want to navigate to. Coronal or Sagittal). all the pixels that already belong to the active mask and which don’t have a gray value within the range. will be added to the active mask. When you move the edit cursor (square/circle/outline) over an image while pressing the left mouse button. pressing this button will update the polyline in the current image. to restore the original threshold after you draw or erased some pixels by mistake… There are 3 threshold ranges. This local threshold tool can be used to remove artifacts in the images. will be removed from the mask. It allows you to reuse the manual editing that you have done on one slice. The middle threshold range is the default threshold that is currently applied to the active mask. the current slice will be copied to all slices above or below the current slice. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. You will notice that all masks are hidden except the active mask.File Menu Page 47 of 74 Draw Erase Threshold Draws in the active mask Erases in the active mask Changes the edited zone back to a local threshold value which is set on the right side. adjust the number of slices the current slice will be copied to and click on one of the arrow buttons. have a yellow color. To use your own threshold range. click on the arrow keys (up or down). areas where some drawing or erasing has been done can be restored to their original threshold. This default threshold cannot be changed.htm 2/3/2014 . The difference with the threshold function in the Segmentation menu is that the one from the segmentation menu is a global threshold that applies to every image in the data set. The intersecting parts of the temporary and active mask are colored in a third color. Multiple slice edit The multiple slice edit tool is great to remove scatter easily. You can still adjust the temporary mask on the other slices and then use this new result again for copying to other slices. double click on a threshold value. When the default values are used. The original mask. meaning that you apply a threshold in a particular area of one image and not on the other images in the project. In the interface. Remove the scatter by selecting the scatter on the temporary mask. If you choose to copy to 0 slices. Note: This threshold is a local threshold. On the other hand. Finally. To copy the temporary mask of the current slice to other slices. You need to repeat the local threshold action on each image that is needed. The multiple slice edit works by creating a temporary mask that can be edited. You can draw or erase pixels from the temporary mask and copy the current slice of the temporary mask on the current slice to other slices. The active voxels of the temporary mask are then added or removed from the original mask or a local threshold is done on the original mask at the active voxels. Note: you can still access the 1-click navigation function by pressing the SHIFT button while you are editing. Then choose to draw on the selected view and you will notice that a new temporary mask is created automatically with a different color. After editing. on other slices. the temporary mask has a purple color and the intersecting parts of the temporary and active mask. the temporary mask is removed or added from or to the active mask or a local thresholding operation is done on the active mask at all the active voxels of the temporary mask. In this example. first choose which slices you want to edit (Axial. every pixel within the square/circle/outline and which has a threshold within the threshold range you set. change the value and press enter.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. release the left mouse button. The difference with the Crop project tool is that even though you restrict your mask. If you set a value different from 0. when you move the mouse now. Determines the operation that will be done on the active mask. If you set the number of slices to 0 you will copy the current slice to all slices before or after the current slice. everything outside region of interest will be removed from the mask. To which slices you want to copy the temporary mask of the current slice. The multiple slice edit interface Type Width/Height Draw Erase Copy to slices Number of slices Shape of the edit cursor: square (rectangle). You can choose between Axial.htm 2/3/2014 . the size will change. The size can be adjusted interactively by keeping the CTRL button and the left mouse button down. To use the Lasso tool: select Lasso as Type.File Menu Page 48 of 74 Remove the pixels in the temporary mask from the original mask. circle (ellipse) or the Lasso tool. you will immediately jump to the last slice where the temporary slice is copied to. where the voxels of the temporary mask are active. Operation on the active mask Crop Mask The mask cropping tool allows you to easily select a region of interest and restrict your segmentation to that region of interest. To end the drawing. Size of the edit cursor (can be different if the Same Width and Height check box is switched off). then draw with your mouse on a slice while pressing the left mouse button. Draws in the active mask Erases in the active mask Determines on which view you can edit the temporary mask and in which view the mask will be copied to the other slices. You can choose to remove the voxels in the temporary mask from the active mask. add the voxels in the temporary mask to the active mask or do a local thresholding on the voxels of the active mask. When cropping a mask. Coronal and Sagittal. the images in the project remain untouched.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. The region of interest is needed to make sure rendering is fast enough. This tool is very helpful when removing scatter and for separating complex structures like vessels. the selected voxels are removed form the mask. You can select or deselect the voxels and by clicking on apply or close.htm 2/3/2014 .File Menu Page 49 of 74 Edit Mask in 3D The 3D mask editing tool allows you to visualize and edit the mask in 3D. The tool works with a region of interest that can be moved and rescaled in the 2D views. You can change the size of the ROI in the Mask tab of the preferences in case you pc is too slow for the default option.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. If polylines need to be updated in a lot of slices you better alter first your segmentation mask in every slice and then recalculate the polylines for the whole mask.File Menu Page 50 of 74 Calculate Polylines The calculated polylines are the high resolution segmentation contours for the current segmentation object identical to how they will be calculated by STL+. Pressing the Calculate polylines button results in the following window: To start calculation. update that polyline in the following way:    Select the Edit tool . Alter your segmentation mask with the draw or erase function. If your selection contains a polyline that has a deformed shape. select the desired masks and click Calculate. Click the Update button or select Update polylines from the Segmentation menu. It can be used to determine the exact threshold value(s) for a correct segmentation. Repeat this in every slice where the polylines need to be updated.htm 2/3/2014 .

Only when you select custom quality you can choose the 3D calculation parameters yourself by selecting the Custom radiobutton. This should be considered when calculating a 3D image. Calculate Click the Calculate button to start calculating the 3D. or on the Segmentation toolbar. Note: You can not calculate a 3D for an empty mask Quality When you calculate a 3D object you can choose the quality. but the dimensions of the 3D will not be accurate because of the matrix reduction that is applied on the images! You will get the most accurate result when you select the optimal quality setting. 3D visualization is performed by means of triangulation of a segmented 3D area. to open the 3D generation dialog.File Menu Page 51 of 74 Update Polylines After changing the segmentation on one layer. The 3D is automatically shown on your screen after calculation. Two methods for reducing the number of triangles are available: Image matrix reduction and/or triangle reduction. The following dialog will pop up: button in the Listed masks Here the created masks (with the lower and higher threshold mentioned) are listed.htm 2/3/2014 . The recommended quality (according to your computer) will be highlighted with a *. click the Options button. Select the masks from which you want to create a 3D. Take low or medium quality if you want a short calculation time. the higher the quality. on the Calculate 3D button in the Masks tab. Options For more information about the 3D generation parameters. The high quality setting will still do a matrix reduction in the XY plane but can give in some situations a smoother and better looking 3D. the complete set of polylines needs to be calculated again. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Here you can set the parameters for the Custom setting for generating a 3D model. The number of triangles determines the quality of the reconstruction: the more triangles. Note: When the threshold value has changed. The downside is that more triangles require more memory. Calculate 3D Click on Calculate 3D from the Segmentation Menu. the current polyline can be updated by clicking this button.

Medium and High settings. With a femur head for instance. All edges of the surface are decided based on the grey values. the resulting mesh gives a noisy surface. Interpolation methods Grey value Interpolation Grey value interpolation is a real 3D interpolation that takes into account the Partial Volume effect and therefore it’s more accurate. However.File Menu Page 52 of 74 A smoothing algorithm changes the overall appearance of the triangular mesh. The advantage of grey value interpolation is that it gives lots of detail and that the dimensions are correct. Contour Interpolation Contour interpolation is a 2D interpolation in the plane of the images that is smoothly expanded in the third dimension. Only if the slice thickness and slice distance are the same. When the slice distance of the scan deviates considerably from the slice thickness. it is recommended to study the 3D generation parameters and to define practical custom settings. Especially for technical CT applications (and all high resolution scans). Grey value interpolation is recommended to use for technical CT applications.htm 2/3/2014 . grey value interpolation works fine. Example of contour interpolation Principle of contour interpolation Conclusion: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. but in the Z direction a linear interpolation between the contours is used (as schematically represented below). Changes of the Z resolution (see the paragraph about Matrix Reduction) therefore should not be used in combination with grey value interpolation. Also the place in between these 2 pixels is based on the grey values of the 2 pixels. With the grey value interpolation method we assume that the bone densities give an indication on the amount of bone within one pixel. you will get better results (meaning: a nicely rounded edge) when using this grey value interpolation. Of course. This condition should be fulfilled during the scanning (acquisition). This interpolation method gives the best results for medical purposes. A reduction of the XY resolution does not violate the condition. it is important to realize that grey value interpolation does not always produce good results. you will need to do a little smoothing as well in order to reduce the noise. The Custom setting is user defined. The disadvantage is that you get unnecessary details due to the noise within the images. This interpolation algorithm uses the grey value interpolation within the slices. Quality All these quality aspects are grouped in the predefined Low.

Matrix reduction This option allows grouping of voxels to calculate the triangles. Smoothing This function is meant to make rough surfaces smoother. Continuity or Accuracy. the number of iterations should be kept low. Slices By default.defined by the user . The Smooth factor indicates the importance of local geometry. Shell Reduction This feature is an extra filter which removes small inclusions by only keeping a number . will give a very nice result. The Reset button will restore the default values. The reduction is given relative to the X-size (= Y-size) of a pixel in the image and relative to the height (Z-size) of a pixel in the 3D data set. If a matrix reduction is set in the plane. every 3D object will turn into a sphere-like object! The number of iterations defines the area of influence for smoothing.htm 2/3/2014 . but when measuring items they will typically appear too large. the local geometry is considered as important and the smoothing is limited. With high values for the ratio (close to 1). The calculation can be reduced to a part of the segmentation by adapting the table positions. If too many cycles are passed. but the 3D can be noisy. A default calculation is a calculation of the whole segmentation. Artificial holes might appear in the 3D image but the dimensions of the object will stay quite accurate. the table positions of the first and the last image are shown in the dialog. Note: When using grey value interpolation. Grey value interpolation is recommended to use for technical CT applications. A Grey value interpolation results always in correct dimensions and correct positioning of the 3D. Don’t exaggerate the number of cycles! All iterations change the triangulation. It works like a filter for noise reduction. STL generation without smoothing STL generation with smoothing Note: If you take a high smooth factor. If this factor is low (close to 0). you have to option to choose the matrix reduction algorithm. Contour interpolation is recommended to use for medical CT applications.or Z-resolution of 1 means no matrix reduction in the plan or the Z-direction. but the 3D dimensions will become larger when using a bigger matrix reduction. The visual representation will be quite good.File Menu Page 53 of 74 A contour interpolation results in a 3D that looks smoother and better (less gaps). reducing too much will lead to incorrect dimensions of the object. Note: When using contour interpolation. XY resolution Decides how many voxels are grouped in the XY plane Z resolution Decides how many voxels are grouped in the Z-direction An XY. The Iteration parameter expresses how many cycles of the smoothing are performed. 2. reducing too much will lead to a loss of information for thin or small objects.of the largest shells. 1. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. In this last case it is obvious that we talk about smoothing. Continuity algorithm Using this algorithm for matrix reduction in the XY-plane. the new position is mainly determined by the position of the other points of the triangles in the neighbourhood.

g. because there will appear gaps in the surface on places where the wall thickness is smaller than the pixel size after matrix reduction. The Edge Angle-value defines which angle should be used to determine edges of the part that cannot be removed. to be part of the same plane that contains the selected triangle. The label will start from the current position and will move upwards. If a plane. It makes sense to keep this value related to the pixel size (e. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Triangle Reduction Triangle reduction allows you to reduce the number of triangles in the mesh. The point reduction and the edge reduction are better for technical objects since they create more uniform meshes. essential part information may get lost. The Edge-type will remove a triangles edge (two points + the connecting line between these two points).File Menu Page 54 of 74 Accuracy algorithm Using this algorithm for matrix reduction in the XY-plane. More iterations therefore do not make a lot of sense. Text size in mm Depth of the text in mm. the program will try to re-triangulate this area. There are three Reducing modes of triangle reduction. Remark: these were also the settings of Mimics 7. medium and high). The Number of Iterations is a user-set value that defines how many times the program should make the calculations.htm 2/3/2014 . use the Set Font button on the right of the Font field. results in a 3D that is less nice. This algorithm converges to a stable result after about 15 iterations. The Working Buffer size relates directly to the amount of memory used to process the reduction. half the pixelsize or a quarter). The advanced edge reduction algorithm generates less noise on the resulting surface and creates a smaller object. The Tolerance indicates the maximum deviation in mm that a related triangle may have. Labels Label Mask Font Size Depth 2D slice-able label Enter label text here The mask that will contain this label Type of text font. The algorithm needs several iterations to reduce the number of triangles in larger flat areas. It is advisable not to use the reducer on very noisy objects. They all have the same parameters. 2D slice-able labels are restricted to horizontal or vertical direction. In this case it is better to perform a smoothing first. The Pointtype reduction mode will try to reduce the amount of triangles by removing a point. To choose a font. defined by the Tolerance and the Angle consists out of several triangles. the Point-type. For the predefined settings (low. the greater the part of the segmentation that can be calculated at once. Triangles deviating less than this angle will be grouped into the plane of the other triangles. The higher the buffer size. where the option to choose between continuity and accuracy were hidden for the user. If the tolerance-value is too big. the Edge-type and the Advanced Edge-type. The positive effect is that the dimensions of the 3D model stay exact. This makes it easier to manipulate the file. then the label will be copied downwards. Mimics automatically selects accuracy for greyvalue interpolation and continuity for contour interpolation. Determines if the label is 2D slice-able or not. unless the top image is reached.3.

The "View from Top/Bottom" is related to the Top/Bottom of the stack of images. When this option is enabled. Calculate polylines from 3D The calculate polylines from 3D will create a polylines set from a 3D object or an STL. The polylines are created by taking the contour of the 3D object or STL on each slice of the project. Calculate mask from 3D The calculate mask from 3D will create a mask from a 3D object or an STL. The source 3D object or STL and the target mask can be indicated in the dialog. Source polyline set and target mask are set here.htm 2/3/2014 . which will delete this label. your new mask can be a bit larger as the original mask. To further edit or delete the created label. and the function Properties. A pane appears with the function Delete. Keep the left mouse button down and place the label in the desired position (this can be done in all views). which will display the Label Properties Dialog box. You can move the label on the images (the mouse cursor changes to a cross). Labels can be exported in STL format in any direction (don't check the 2d slice-able label button). fills polylines that are calculated from a mask and interpolated during this calculation. The labels might look incorrect in the 3D View of Mimics. The mask is created by taking the contours of the 3D object or STL on each slice of the project and then by filling the contour with a mask.File Menu Page 55 of 74 Horizontal or Vertical Orientation of label View from top or View from Bottom Orientation of label Note: Changing the font of labels is not possible with 2D slice-able labels. check the 2D slice-able label button. Cavity Fill from Polylines The cavity Fill from Polylines will create a mask by filling every polyline in a polyline set. Note: Please be aware that because the cavity fill from polylines. the labels are restricted to horizontal and vertical direction. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. If you want your labels to be visible in exported sliced files. click the right mouse button on the label.

select to register STL1 on Mask1 and that STL2 should move. If you e. To use this function. List of Landmark points Name Add Point Name of the object. 3D Objects and images. Lists if the contour of the object is visible on the 2D slices or not by means of glasses.g. To register an implant with the point registration. By clicking on the name of the object. Allows you to add a set of landmark points. it can be changed. Lists if the STL will move when registering another STL. You can change the visibility of the contours by clicking on the glasses. You can do this by left clicking on the images or on a 3D object or STL to indicate the point that has to be moved and then by doing the same operation to indicate the point where the first point has to move to.File Menu Page 56 of 74 Registration Menu This menu contains the following items: Point Registration The point registration allows you to easily move an STL to a certain location. place landmark points on both objects. This will open following interface: List of STLs Name Visible Contour Visible Move Name of the object. By clicking on the name of the object. it can be changed. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm 2/3/2014 . Mimics will then calculate the transformation matrix that should be applied to have the best fit between the start en end points and applies that transformation matrix on the selected STLs. first load an STL (File Menu -> Load STL). Then go to the Registration menu and choose the Point Registration function. This is done by placing one or more sets of landmark points on the STLs. Lists if the object is visible or not by means of glasses. STL1 will be registered on Mask1 and the same transformation matrix will be applied on STL2.

htm 2/3/2014 . first load an STL (File Menu -> Load STL) and create a mask of the feature on which the STL should be registered. Lists if the object is visible or not by means of glasses. You can change the visibility of the contours by clicking on the glasses. select to register STL1 on Mask1 file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. it can be changed. Then go to the Registration menu and choose the STL Registration function. Lists if the contour of the object is visible on the 2D slices or not by means of glasses. Lists if the STL will move when registering another STL. If you e. To use this function.g. STL Registration The STL Registration function allows you to register STLs on masks. By clicking on the name of the object.File Menu Page 57 of 74 And apply to find the best fit between the landmark points and to move the STL to the new location. This will open following interface: List of STLs Name Visible Contour Visible Move Name of the object.

STL1 will be registered on Mask1 and the same transformation matrix will be applied on STL2. Residual Error The residual error gives you an indication of how good the position of your STL is with relation to the mask. only points that have a distance that is higher than 1mm from each other will be taken into account. By using the Mimimal point distance filter. make sure that your STL is already located in the neighbourhood of your mask by using the Translate and Rotate button on the STLs tab in the Project Management. To use this function. Settings You can choose to do a Global Registration or a Local Registration. Note: Before doing an STL registration. you can define this distance. The error is a qualitative error. The file with the transformation matrix will be saved in the folder of the Mimics project. The local registration will only work if your STL is already positioned correctly. By specifying the Maximal distance to mask border filter. enter a filter value of 1mm. you have to first open the base dataset that you want to use for the registration. When registering an STL. If you e. This will open following interface: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Local Registration The local registration will only work on all points that are within a certain distance of the border of your mask. you want to do a global registration first and if you would then like to do a feature-based registration. Then go to the Registration menu and choose the Image Registration function. Using a filter value will make sure that your result is independent of the density of the STL and will speed up calculations. Global Registration The global registration will work on your whole STL. you can use the local registration.g. after doing a registration. In general. Mimics will also write out the transformation matrix that was applied during the registration.htm 2/3/2014 . you can just give it a value of 0mm. Lists if the object is visible or not by means of glasses. so you can only use this value for comparing the result when changing the parameters of the registration. Higher Threshold Higher Threshold setting of the mask. By clicking on the name of the object. If you don’t want to use the filter. Lower Threshold setting of the mask. List of Masks Name Visible Lower Threshold Name of the object.File Menu Page 58 of 74 and that STL2 should move. it can be changed. you can choose not to use all points of your STL. Image Registration The Image Registration function allows you to fuse two datasets by doing a landmark point based registration.

Landmark Points file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.File Menu Page 59 of 74 Load in the second dataset Next you can load in the dataset that you want to fuse with the base dataset by clicking on the browse button. You can also use the toolbar at the top for panning. When you have chosen the second dataset. Mimics will show this dataset in the views on the right: You can use the keyboard and mouse shortcuts for panning. You can browse through your harddisks and choose a second dataset from this interface. This will open the open project dialog. scrolling through the images. adjusting the contrast. zooming. zooming.htm 2/3/2014 .

GVr = GV1 x GV2 If GVr is higher than 4095GV. GVr = GV1 AND GV2 A bit wise AND is done of GV1 and GV2.File Menu Page 60 of 74 You can add landmark points by clicking on the Add button. GVr = Abs(GV1 . You need at least 3 landmark points to be able to do the registration.GV2) The absolute value is taken of the difference between GV1 and GV2. Export Menu This menu contains the following items: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. it is set to 4095. GVr = Maximum(GV1. GVr = GV1 / GV2 GV1 is divided by GV2. Fusion Method You can select different Fusion Methods from the list: Add Subtract Multiply Divide Difference Average Min Max AND OR XOR Transparent Opaque GVr = GV1 + GV2 If GVr is higher than 4095GV. GVr = GV1 XOR GV2 A bit wise XOR is done of GV1 and GV2. GVr = Minimum(GV1. it is set to 0.GV2 If GVr is lower than 0GV. the right-click in one of the views of Dataset 1 and then right-click in one of the views of Dataset 2. GVr = (GV1 + GV2) / 2 The average is taken of GV1 and GV2. Applying the registration When you have placed at least 3 landmark points and you have chosen your fusion method. The landmark points can be moved by left-clicking on one of the landmark points in the views and dragging the points. GVr = GV1 x (GV2 / 4095) The grayvalue of Dataset 2 is determining the transparency of the voxels of Dataset 1. The result is that Dataset 2 is transformed to the coordinate system of Dataset 1. you can apply the registration. it is set to 4095. You can delete and locate landmark points by selecting the point from the list and clicking on the appropriate button. Dataset 2 will be resliced and registered and the part intersecting with Dataset 1 will be fused with Dataset 1.htm 2/3/2014 . Mimics will then create a new Mimics project that is as big as Dataset 1. You can however choose to use more points. GVr = GV1 .GV2) The maximum is taken of GV1 and GV2. GVr = GV1 OR GV2 A bit wise OR is done of GV1 and GV2. GVr = GV2 The grayvalues of Dataset 2 are used.GV2) The minimum is taken of GV1 and GV2.

File Menu Page 61 of 74 Dicom Allows converting the axial images into Dicom format. 3dd Allows exporting a mask to a 3dd file. You can choose a mask from the list. BMP/JPEG Allows exporting to an image file. Then you can choose an output directory by clicking on the Browse button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Browse to a directory where you want the Dicom files to be saved.htm 2/3/2014 . You then have to fill in a file name in the File name input box.

g..htm 2/3/2014 . bmp or jpg. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. You can also choose the type of image file you want to save. By selecting Grayvalues in the Export menu. You can choose to export the Axial. Sagittal image and if available. "Axial-523.. "Axial". a dialog is displayed where you can choose to export masks as a textfile with all the grayvalues of the voxels. . e. the Parallel or Cross-section image.g. e.bmp".bmp". Description of the main areas Select a mask to export in Grayvalues Output directory This area displays the masks that are currently available in your project. You can easily choose the path where the image files will be saved with the Browse button. You can also export a range of slices. in the filename input box. Select here the desired mask to process. The image filename will be constructed with the root name and the slice number. Grayvalues Allows exporting a text file with the grayvalues of your images.File Menu Page 62 of 74 The export of the 2D image(s) is an image that contains the correct pixel size and can thus be printed in a 1:1 ratio. Coronal. "Axial-521. You need to fill in the root name of the filename.

or only one of the views. you can choose the framerate of the movie and the codec that is used to export the movie. You can change the file name of your Grayvalues file. The filename of the movie that will be exported. If the auto rotate function is on. In the options menu you can choose some general options and some options for the movie itself: You can choose to minimize the application during recording. When you click on the stop button or on the close button. Choose between Hounsfield units and Grayvalues. When you go to the export menu and choose movie. When you click the browse button you select the location where you want your movie file to be placed. pause and stop it. to capture the mouse cursor. Movie The export movie option allows you to export a movie of your Mimics User Interface while you are working. It will act like the Windows Explorer. your 3D view will be rotated 360 degrees and this will be exported to a movie.File Menu Page 63 of 74 File name Save as type Expressed in When you click the button a window appears. Select the location where you want your Grayvalues file to be placed. following interface will appear: Description of the main areas Function buttons Options With these buttons. play the movie after recording and to use the auto rotate function. you can start the recording. In the movie options section.htm 2/3/2014 . You can choose to capture the whole application. At this time the only possible output format is txt (textfile). You can look at all the drives of your computer and their directory structure. View to capture Output Directory File Name Options Menu file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. the current movie file is closed.

File Menu Page 64 of 74 The Options menu contains the following items: Licenses In the Registration dialog you can display your current license situation. Settings about visualization of the indicators. request passwords and register new modules. the 3D reference planes. the 3D reference planes.. On-line reslicing is the calculation of the cross-sectional images and parallel images based on the axial images. Possible preference settings are: General Visualization 3D Masks Predefined Thresholds Annotation Printing Reslicing SCSI General settings like undo settings. Preferences In the preference dialog box you can set your preferences that will be applied every time you start the software. Settings about colors and names of masks Settings about the Predefined Thresholds of the threshold toolbar Settings about the font and background of the annotations Settings about the pages and objects to print. Settings about the on-line reslice. performance settings. go to the Options menu and choose Licenses..htm 2/3/2014 . performance settings.... More information on how to register can be found in the Register section of the Introduction chapter... Settings concerning the 3D: the type of rendering. Settings concerning the 3D: the type of rendering. General preferences file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.. autosave settings.... view. To display the Registration dialog. display contact information..

Preformance Always ask to reduce images when loading Maximum Undo Disk Space Autosave Settings Select this option to have the Reduce Images dialog always displayed when importing images or when opening a project. You can look at all the drives of your computer and their directory structure. . Pixel Unit HIPAA Hide Filename Hide Patient Name Select this option to hide all file names.. When opening the software again. This gives the frequency that the project will automatically be saved. in the open project window. you will still see the patient name. You can look at all the drives of your computer and their directory structure. Select this option (in combination with the "Hide file name" option) to work in compliance with HIPAA. The patient ID contains the initials of the patient and a unique number. The patient name will be replaced by a unique patient ID in the project information window.. More information about the reduction of images can be found on the Reduce images page..htm 2/3/2014 . the project information window. When you export the images to Dicom files and open the images with a Dicom Viewer. the other user can turn off the “Hide patient name” option to see the patient name. the print preview. Allows you to choose between a GreyValues scale or a Hounsfield scale. the open project window. The patient ID cannot be changed. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. loading and saving projects. Select the desired directory. Included is also an autorecovery function when an unexpected event like PC failure would occur. Select the desired directory. It will act like the Windows explorer. it will recover your project you were working on.. When you click the button a window appears. etc. Note: this function only hides the patient name. It will act like the Windows explorer.. . When saving the study. Indicates the maximum disk space that will be used to store information for the undo and redo operations. When you click the button a window appears.. STL Library Working Directory This directory will act as the root directory for the STL Library. when you exchange the file with another Mimics user. Because the initials are still in the patient ID you can easily differentiate between the different patients. the printed documentation. the proposed file name will be the patient ID instead of the patient name.File Menu Page 65 of 74 Working Directories Default Working Directory This directory will act as a default for all actions concerning importing of images. without having to keep a list with patient ID and associated patient name. . Or. Select a time frequency from the drop-down list.

the intersection lines. In the 4 panes view. View You can choose between 3 or 4 panes.File Menu Page 66 of 74 Image When selected Mimics will use less memory for the visualization of the images. In the first case the 3D will replace the sagittal image in the image layout and the axial image in the reslice layout. the Toggle 3D button is not present. 3D preferences file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. In that case. You can also choose if you want to see all cross-sections or only the active cross-section and if you want to see full lines or dashed lines. the slice position and/or the orientation strings on your screen. you will see all image views and a 3D view. Visualization preferences Default Indicators You can decide if you want to see the tick marks.htm 2/3/2014 . User Interface To restore the interface items to their default settings click the appropriate restore button.

This setting can not be selected if you chose Software rendering. because the software will look for the card and use the memory on the card for visualization.htm 2/3/2014 . invisible Hide all 3D when opening a project Use this option for faster loading of projects. All 3D objects will be set invisible when you open a project when this option is enabled. the rotation will always be done around an axis perpendicular to the axial images. You can set the specular reflectivity of the 3D objects. select OpenGL or Direct3D (Use hardware not selected) or Software rendering. These planes indicate the current position of all the image views in 3D. Masks preferences file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Reference planes Select the reference planes to be shown in the 3D view. When the setting is enabled. Enhances the 3D visualization. This setting chooses the rotation axis of your 3D object.File Menu Page 67 of 74 Rendering Select OpenGL or Direct3D rendering and select Use Hardware if you have a graphical card with hardware acceleration. With this renderering you get an optimal graphical visualization. Visualization and navigation 3D background color Use Gouraud shading Specular reflectivity Use world axis rotation Defines the background color of the 3D view. Faster 3D interaction Will switch the 3D to a simplified representation when the frame rate drops below the selected value. If you don’t have a graphical card with hardware acceleration. To change this color click on the colored square. Performance Unload 3D from memory when Frees the memory when the 3D is not shown.

Predefined Thresholds file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm 2/3/2014 . Allows to change the name tag of the selected mask All 3D objects will be put on invisible when you select to edit the mask in 3D.File Menu Page 68 of 74 Here you can adjust the default colors of the masks. Default mask names and colors Color Name Edit Mask in 3D ROI size Hide 3D objects Region of interest Restore Restores all mask preferences to its default settings. Allows you to change the color of the selected mask. reducing the ROI will make the visualization faster. The 3D mask visualization tool is a demanding feature. Allows you to set the dimensions of the region of interest.

Resets the values of the predefined threshold to their original settings. selected in General preferences. Edit Predefined Threshold setting Edit Add Delete Reset Move Up Move Down Allows you to change the name. Deletes the selected predefined threshold. Moves the predefined threshold down in the list.htm 2/3/2014 .File Menu Page 69 of 74 List of Predefined Thresholds Name Lower Threshold Higher Threshold Name of the predefined threshold Indicates the Lower Threshold in the pixel unit. Annotation file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. Indicates the Higher Threshold in the pixel unit. Moves the predefined threshold up in the list. selected in General preferences. Allows you to add a new predefined threshold. the Higher and Lower Threshold value of the selected predefined threshold.

Allows you to choose the background color of the annotation box.File Menu Page 70 of 74 Visualization Font Box Background color Allows you to change the font of the annotation. Select Modify… to visualize the Font selector dialog. Printing preferences file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm 2/3/2014 .

Reslicing preferences file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm 2/3/2014 . If the cross-sectional spacing in the prints is not the same as in the images a message will appear about measurements that may not be visible anymore. Distance between images Spacing between the cross-sectional images and the parallel images in the prints. Objects to print Select the objects to print.File Menu Page 71 of 74 Print Pages Select the pages to print.

File Menu Page 72 of 74 Reformatting images Distance between cross-sections Spacing between two cross-sections. Advanced SCSI file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. . X-ray depth The thickness used to calculate the parallel X-ray. Distance between parallels Spacing between two parallel images Maximum movement range The maximum range of movement for the parallel on both sides of the one that is originally drawn. The real range can be different on both sides: the real range is limited so that the parallel curve does not self-intersect. the cross-sectional images will be shown at the exact position (see blue dotted line) and not to the fixed position nearby (cyan colored cross-sectional. This originally drawn curve is at position 0. while it will be the maximum range at the outside of the bend. Snap to fixed positions of cross. number 5). the movement range inside this bend will be very limited.If you don't select this setting you are able to navigate to virtually every position you want.htm 2/3/2014 . If you draw a curve with a sharp bend. Take a look at sectionals the picture below. When you click on the position like indicated with the red bullet. Cross-sectional grid Defines the cross-section grid.

If it is not linked to a SCSI device. When you click on the Start Auto Test button the available services will be automatically marked. The software will then check which of these are linked to a SCSI device by sending them a command.File Menu Page 73 of 74 To enable Mimics to import Data from a SCSI MOD or Tape reader select enable SCSI. select the service and click on the Test button. If you want to import from a SCSI device (e. all SCSI communication is disabled by default. The "SymEvent" driver of Symantec for example has this effect. Mimics can auto determine which SCSI devices to access therefore select auto determine and click on start. you have to enable SCSI in the advanced SCSI dialog.htm 2/3/2014 . Mimics will try to detect all the services running on your system. It gives you the possibility to enable or disable sending the command to some of the services. When a service is linked to a SCSI device. Note: when Mimics is installed. All the services with a check mark next to them will receive the command. Help Menu The Help menu contains the following items: You will also find the corresponding buttons in the toolbar. A problem found is that some of these services just generate a system crash when replying to this command. This List box displays a list of all the services present on your Windows system. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. If you want to test a particular service.g. it will ignore this command. a MOD or Tape drive). it will respond with a certain message. Symantec has created a patch for this problem but some other services may also be buggy.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD. The cursor will change to this: Click on a button or a menu item to open the help page about that specific subject. please forward it to Materialise together with your system information.File Menu Page 74 of 74 General Help Select Help | General Help from the menu to start the help pages at the home location. Context Help   Click on the Context Help button or select Help > Context Help from the menu. will start the help pages at the tutorial location. If you encounter any problem with the software. .htm 2/3/2014 . Example: Opens the help page about the Toggle 3D button. About Mimics The About dialog box displays some information about the system you're working on. Opens the help page about licenses.

if you want to import Dicom images from an Elscint optical disk you need an Elscint import license. If you want to import native Siemens images from CD you need a Siemens import license. floppy. Importing Dicom. CD.htm 2/3/2014 . When the data is stored on an optical disk or tape you also need an optical drive that can read the optical disk or tape. The images can be read from hard disk. depending on      The type of images you want to import from hard disk or CD The type of MOD or tape No license is needed when you Import images manually Import Tiff or Bitmap images Import Dicom images from hard disk or CD For example.Import Page 1 of 169 Import The import modules allow you to convert images from a variety of scanners to the Mimics file format. Importing images from hard disk. The provided modules are: Siemens import GE Advantage import GE DAT import Philips import GE YMS import Dicom import Toshiba import Picker import Elscint import module for Siemens scanners module for General electric scanners module for General electric scanners. Tiff and Bitmap images from hard disk or CD doesn’t require a license. More details can be found on the import licenses page. but license passwords are required for all other images that you want to import automatically. CD. Links to the sites of the different drivers and some hardware specifications can be found in Hardware Specifications. More details about the scanners and the devices supported by the Import module can be found in Overview scanner formats. Start Mimics and open the Import images wizard by selecting Import images from the File menu. import some images and Mimics will display the required module. Each module can be registered separately or combined. If you don’t know what module you need. the drive should file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Import licenses To convert images you need one or more licenses. DAT medium module for Philips and Hitachi scanners module for Yokogawa Medical Systems scanners module for DICOM format module for the IS&C format of Toshiba scanners module for Picker format module for Elscint format Reading from Optical Disk Reading from optical disk Connect the optical drive to your computer and start your computer. MOD and tape is very easy using the Import images wizard. optical disk or tape. If your computer recognized the drive.

read the Hardware configuration for SCSI devices page. Hardware configuration for SCSI drives Hardware configuration for Pioneer DE-7001 series At the back of your MO-Drive (Pioneer DE-7001 series) you will find a DIP-switch containing eight small switches as shown in the next figure. You can click immediately on the drive icon or you can browse for the drive in the Windows Explorer tree. Never change these switched without switching the drive to power-off. as long as the computer performs no operations while the drive is still switched off. except those to change the SCSI address or those to change the drive operating mode. click Next and continue the wizard like described in Step 2 of the Import images wizard page. read the SCSI troubleshooting page or the Frequently Asked Questions page. you need to have Administrators rights in order to access the SCSI devices.MO) The first three switches are used for selecting the scsi address. Keep all switches in the position as marked in this figure. When you need help configuring your SCSI device. Remarks:   If an optical disk is DOS formatted you can access the disk via My Computer > Removable drive. the last two for selecting the operating mode of the drive (WORM mode or MO mode).Import Page 2 of 169 already be listed in the favorites list. this will also be listed (see picture). A list with the attached SCSI devices will be shown. Select in the tree the SCSI Adapter to access to SCSI devices.htm 2/3/2014 . SCSI address Operating mode (WORM . When the Import module recognizes the disk or tape format. When you have Import problems. When you work on Windows NT. (It is not needed to switch off the computer.address. Select at the right side of the window the images on the optical disk to convert.) Setting up the SCSI. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

you will find a SCSI address selector switch. The switches 4 and 5 are used to select the operating mode of the drive. At any time. the drive is in WORM mode. the switch positions in the previous figure give an address of 2. when in the Off position (and a value of 0 when in the On position). the drive is in WORM mode.address. At the left side of the power button. and put switch 2 (value 2) to Off. the selected address is displayed within the window between both buttons. the drive is in MO mode.Import Page 3 of 169 The switches 1. The drive has to be set as follows: If there’s no SCSI II mode.) Setting up the SCSI. The switches 7 and 8 are used to select the operating mode of the drive. Never change any of these switched without switching the drive to power-off. 2 and 4 res. If the SCSI card has SCSI II mode. An x in the figure means that that side of the button is pressed in. keep all switches in the position as marked in this figure. the driver automatically swaps between MO and WORM mode when necessary.switches on the SCSI address selector will increase res. except those to change the drive-operating mode. Selecting the operating mode ( no SCSI II mode ). the drive is in MO mode. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Always keep switch 5 in the off position. Pressing the + or .htm 2/3/2014 . So to calculate the SCSI-address you have to add the values of the switches in the Off position. put the switches 1 (value 1) and 3 (value 4) to On. When switch 8 is in Off position. you will find a SCSI address selector switch. (It is not needed to switch off the computer. the address is then 1 + 4 = 5 ! Selecting the operating mode. 2 and 3 have the values 1. To generate an address of 5. e.g. decrease the SCSI address. as long as the computer performs no operations while the drive is still switched off. Hardware configuration for Pioneer DE-7101 series At the back of your MO-Drive (Pioneer DE-7101 series) you will find a DIP-switch containing five small switches. At the left side of the power button. Always keep switch 7 in the off position! When switch 8 is in On position. Keep all switches in the position as marked in this figure. When switch 4 is in Off position. Hardware configuration for LMSI LD 520 series At the back of your MO-Drive you will find a DIP-switch containing eight small switches as shown in the next figure. When switch 4 is in On position. except those to change the SCSI address or the one to change the drive operating mode.

Selecting the operating mode.) Setting up the SCSI. 2 and 3 have the values 1. So to calculate the SCSI-address you have to add the values of the switches in the Off position. Keep all switches in the position as marked in this figure. the switch positions in the previous figure give an address of 2.address Pressing the + or . The settings as in the figure below should be correct. if your cables are still OK the dip switch settings of your device You're working on NT When you work on Windows NT. When switch 7 is in On position. the drive is in MO mode. switch 7 for selecting the operating mode of the drive (WORM mode or MO mode). except if you need to change the termination settings. This list typical displays the SCSI addresses that are in use and will also display the brand name of the attached devices.htm 2/3/2014 . the address is then 1 + 4 = 5. (Check with your drive manual for these settings. decrease the SCSI address. Hardware configuration for Hitachi OU152S-1 series At the back of your MO-Drive (Hitachi OU152S-1 series) you will find a DIP-switch containing 4 small switches as shown in the next figure. When switch 7 is in Off position. At any time. 2 and 4 res. The switch 7 is used to select the operating mode of the drive. (It is not needed to switch off the computer. the settings are file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. check: if you made a correct termination of your devices If you made a correct daisy chain when working with several devices. you see your device(s) in the list that will appear on your screen. SCSI Troubleshooting You don't see drives in the SCSI Adapter list It can be a hardware configuration problem Make sure when that when you boot your system.) Setting up the SCSI.) Right below the DIP switch you will find a scsi address selector as shown in the figure below. To generate an address of 5. If you don't see your device here. Typically for the HP kayak. and put switch 2 (value 2) to Off.g.Import Page 4 of 169 The first three switches are used for selecting the scsi address.switches on the SCSI address selector will increase res. Never change any of these switched without switching the drive to power-off. the selected address is displayed within the window between both buttons. Never change these switched without switching the drive to power-off. as long as no operations are performed by the computer while the drive still is switched off. The switches 1. (It is not needed to switch off the computer. the drive is in WORM mode. You have SCSI Wide You will need to change some settings in the BIOS of your machine. when in the Off position (and a value of 0 when in the On position). put the switches 1 (value 1) and 3 (value 4) to On. e. as long as no operations are performed by the computer while the drive still is switched off.address. you need to have Administrators rights in order to access the SCSI devices.

This will probably solve your problem. set "Initiate Wide Negotation" to NO. check if you see the devices listed together with their SCSI address. Sometimes there is also a fifth file containing some images. check the Advanced SCSI Options (for Windows NT) Unknown medium This might sound stupid. Each module can be registered separately or combined. Typically all images are stored in one file that is the fourth one on the tape. The conversion is then similar as Importing images from hard disk. check if you have the correct drivers for your SCSI card. the conversion still needs to be performed. You get the message that you have no license to run this converter In order to access data via SCSI interface. Picker tapes are tapes that can be dumped using the Eliant 820 from Exabyte. press <Ctrl><A> for the SCSI Select Utility . Reading from tape Dumping data from tapes must not be confused with the automatic conversion of GE HiLight Advantage tapes. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 . When the files from a tape are dumped. this line is shown: "EXABYTE: Picker tape". When you boot your PC.Import Page 5 of 169 set to SCSI wide (32 bits). Blue Screen on pressing import button When you have a blue screen from the moment you click on the Import button. If they still don’t appear in the list. you need to change that (for the SCSI address that you will use) to SCSI narrow (16 bits): Example for an Adaptec AHA 2940 SCSI card in an Alpha PC: When you boot the PC.(This message is displayed when booting. extra passwords are required. Save the new settings. look for something similar) Select from the menu : "Configure/ View Host Adapter Settngs" Select from the menu : "SCSI Device Configuration" Now you see a list of all the available SCSI addresses. for the ones you will use for the device drivers. The third 'file' on a Picker tape is some blank data that needs to be skipped. Picker tapes can be read as follows: Click on SCSI Adapter. but also try reading the other side of the disk.

The dump file is stored in the Target directory you’ve set in the Tape Dump Parameters window. The following parameter window is displayed: Since typically all images are stored in the fourth file (or partition). file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 .Import Page 6 of 169 Select this line and click on the Dump button .dmp extension) that needs to be converted afterwards. follow the instructions as described in the Import section of Mimics (see picture below). It is this "Dumpfile" (with *. you need to dump this file. To import this dump file.

Then you need to try out yourself on what partitions the data is stored. Answer No to stop reading. you get the message: When the end of the tape is reached. the following message is displayed. If there are no other readable partitions on the tape.htm 2/3/2014 .Import Page 7 of 169 Other tapes than Picker tapes can be dumped as well in a similar way. Several messages can appear while dumping the tape. It means that 6 dump files have been made. If Mimics is reading an empty partition you get the following message: Answer Yes if you want to skip the empty partition and continue reading the next partitions. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

Import Page 8 of 169 Dicom Input Application The Dicom Input Application allows you to receive Dicom images that are sent via a Dicom network. Continue the import operation following the Installing the DIA The DICOM Input Application or DIA is a licensed feature that allows you to receive images via a DICOM network.htm 2/3/2014 . click the DIA button to visualize the images stored in the DIA folder. . When new images are received. In the Import Images Wizard. following dialogs will be shown: STEP 1: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. When the Dicom input application is installed and licensed. We recommend that you close all other applications before installing the DICOM Input Application. If you are running Windows NT or Windows 2000. you need to update the DIA database by clicking on the Rebuild DIA Database button steps described in the help pages about the Import Module. When Dicom images are received. a message will be displayed to inform you. Start the wizard by selecting Import Images in the File menu or by clicking on the Import button in the toolbar. During the installation of the DICOM Input Application. Then select the files to import and click on the Next button. The received images can be viewed via Windows Explorer or via the Import Images Wizard. you must have administrative privileges to install the software. you will notice a yellow folder icon on the bottom right corner of your desktop. The Dicom images are stored on your computer in a local folder (DIA folder). which can be chosen during installation.

STEP 3: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 9 of 169 Wait until the progress bar is finished and then click Next to proceed. STEP 2: After reading the license agreement. click the Yes button.htm 2/3/2014 .

Import Page 10 of 169 The DICOM Input Application will be installed in the directory: C:\Program Files\Materialise\DICOM Input Application. If you want another folder name. Click Next to proceed. select an existing directory by clicking on Browse. If you prefer another directory. STEP 5: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. STEP 4: Program icons will be added to the Program Folder > Materialise Software. then type a new name or select one from the existing folder list.htm 2/3/2014 .

STEP 7: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. click Browse and choose a new destination folder. If you want DIA to use another folder. STEP 6: The installation program suggests a folder on you computer to store all images that will be received via a DICOM network. IP address and port number assigned by your network administrator. Click Next to proceed if you agree with the chosen folder. Click Next to proceed.Import Page 11 of 169 Enter the workstation’s AE Title.htm 2/3/2014 .

htm 2/3/2014 . click Next to proceed. Click Finish to close the installation dialog. This window will close automatically when the progress bar is finished. STEP 8: The DICOM Input Application gets installed. This can take a few moments. STEP 9: The software is successfully installed. STEP 10: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. It’s recommended to reboot your computer to finalize the installation. If you want to change or review something.Import Page 12 of 169 When everything is filled in like you want. click Back.

slice distance…). Overview of supported images DICOM Mimics supports the latest DICOM 3. The DICOM format is a standard in the Medical Imaging world and most recent scanners areDICOM compliant. patient name). BMP. we also offer different Import file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Both lossy and lossless JPEG compression is supported. go to Start > Settings > Control panel > Add/Remove programs.htm 2/3/2014 .g.0 and 2. All DIA folders will be removed. please look at the Registration help page. To uninstall the DICOM Input Application. image size. The only restriction when importing images manually is that the images have to be uncompressed. the DICOM Input Application will start automatically and will ask you if you want to register it. For more information about the registration process. The properties of these images are recognized automatically and you only have to fill in the information about the data set (e.0 standard but also previous ACR-NEMA formats (1. Even DICOM images made with cone beam scanners from Morita and NewTom scanners and proprietary images made with cone beam scanners from Aracor are supported.0). Select DICOM Input Application and click the Remove button. you can also do a manual import of the images.Import Page 13 of 169 When you reboot the system. User-defined Import If the image format is not supported but you know all the properties of the images (pixel size. Mimics can import DICOM images that are compressed with the JPEG algorithm. TIFF Mimics supports BMP and TIFF images. Proprietary Formats Beside these image formats that are supported by the Mimics base module.

If your scanner is not on the list. It could be that we already support your scanner or that we can provide you with a solution for your type of scanner. you can import several proprietary formats from scanner manufacturers. SR Picker MxTwin Picker PQ.Import Page 14 of 169 Modules. PQ 5000. QX/i. LX/C. Dual. Plus. RP GE Lightspeed. ZeusRP GE Hilight Advantage GE HiSpeed. Supported Scanners Asahi Roentgen PSR9000N Elscint CT twin Elscint Elite Elscint Exel 2400 Elscint Omnipro Elscint Twin GE 9800 GE Advantage GE CT/e. Below you can find a list of some of the scanners. devices and media we support.htm 2/3/2014 . Different types of media and devices are supported. please contact us. 2000. CX. TX. Ultra GE Prospeed GE Sytec GE CT Pace GE Sigma (MR) Hitachi MRP 7000 Hitachi W2000 Hitachi W950 Philips Aura Philips Brilliance Philips Easyvision * Philips Mx 8000. 16. IDT Philips Secura Philips Tomoscan 60/TX. QX/i. CX/Q. PQ 6000 Shimadzu SCT Siemens Balance Siemens Emotionm Duo Siemens Esprit Plus Siemens Magnetom (MR scanner)* file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Zeus. With every Import Module. Dual GE GEMS Jupiter. LX. CX/S.

htm 2/3/2014 . Sony. 10. 4mm DAT tape 8mm DAT tape Maxell LM510 Maxell OC-112P-2 Maxell OC-112P-2 MaxOptix Pioneer DC-17GWO Pioneer DC-502 Pioneer DEC-17GMO Pioneer DEC-702 Verbatim file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. 16 Siemens Somatom 4 AR *... AR*. 6.Import Page 15 of 169 Siemens Sensation 4. DRH*. Verbatim.25 inch MOD like MaxOptix. 4 Plus. HiQ*. Plus* Siemens Volume Zoom * Toshiba Toshiba Aquilon Toshiba Asteion Toshiba IS&C Format Toshiba Xpress Toshiba Xvision Yokogawa ProSpeed Supported Devices 4 mm tape drive Exabyte Eliant 820 (8200 format) Hitachi 5” Optical disk drive type OU152S-1 LMSI LD 520 MOD-WORM devices Max Optix drive type T4-2600 Max Optix drive type T5-2600 Pioneer DE-7001 series Pioneer DE-7101 series Pioneer DE-H9101 series Sony RMO-S551 Supported Media 5. AR/SP.

Both the generation (automatic or manual) and the removal of these support structures are complex problems: not enough or not strong enough supports are causing inaccuracies.maxoptix. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. More information about the devices can be found on following web-pages : MaxOptix drives: http://www. the support structures can be designed in the CAD system. One of the major difficulties in Stereolithography and most other Layer Manufacturing techniques is the need for support structures.sel. sometimes exceeding the drawing work of the part itself.exabyte. More information about the devices can be found on following web-pages : MaxOptix drives: http://www. this deformation can be minimized. This means that there is no surface information available and the standard techniques for automatic support generation cannot be used. CLI for Eos).com/ Pioneer drives: http://www. Optimal accuracy is achieved in a very short time by the direct conversion of the images to several sliced machine file formats: SLI and SLC for 3D Systems.jsp?taxonomy_id=43 Exabyte. Patient information can be displayed by a punched or colored label.jsp?taxonomy_id=43 Exabyte.sony. giving an extra dimension. This is the case in medical applications where the layer information of the CT scanner is interfaced directly to the layer information of the Stereolithography machine. Eliant 820 tape drive: http://www. Another function of the supports is to reduce curling effects.exabyte. Stereolithography resins have a tendency to deform during the building process because of internal stresses generated by the shrinkage. always check on the physical compatibility between the disk and the drive.com/pioneer/deskpage. Eliant 820 tape drive: http://www. The basic function of the support structure is to support the part during the building process. one is not able to generate a support starting from an STL description. In addition the manual generation of the supports is impossible because the information is not present in a CAD system. too much or too strong supports are resulting in bad surface quality and/or a lot of cleaning work. When Stereolithography is used starting from a CAD representation. By building a strong support structure under a part.maxoptix.g.htm 2/3/2014 . For that reason.pioneer-eur.cfm Sony drives: http://www. and 'islands' which are isolated at a certain moment during the process need to be attached with the rest of the part. This is a large work.sel. Magics RP. The whole part is connected with a platform.com/products/products/eliant.Import Page 16 of 169 * Uncompressed image files are required General Remark : Every disk drive has a limited capacity that it can handle.com/ Pioneer drives: http://www.sony.com/SEL/rmeg/data/ General Remark : Every disk drive has a limited capacity that it can handle. e. High order interpolation (bilinear and inter plane) algorithms result in excellent surface reproduction from scan to model.com/products/products/eliant. always check on the physical compatibility between the disk and the drive. contact us. nerve channels can be highlighted in the RP model.pioneer-eur. In some instances however.com/SEL/rmeg/data/ RP Slice RP Slice interfaces from Mimics to Rapid Prototyping systems via sliced files to build models. teeth and teeth roots. If your scanner is not on this list.cfm Sony drives: http://www. RP Slice supports color stereolithography: tumors. maybe we can help you.com/pioneer/deskpage. software was developed in the past to generate automatically support structures starting from an STL description of the part.

All files in this queue will be exported in the selected output format and will be saved in the selected output directory. Select a contour format (CLI. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. SLI or SLC) from the Export menu. This module allows you to calculate contour files and support structures starting from these contour files. Note: If you're not able to start RP Slice. 3dd files and contour files. you probably haven't entered the passwords yet. 3dd files or contour files. Starting RP Slice All RP Slice functions are loaded immediately in Mimics after registration of the RP Slice module. When no project is opened in Mimics or when only the STL+ module is licensed (and not the Mimics basic module) you can only select 3dd or contour files. Remark that you are not allowed adding a combination of masks. By clicking the Add button you add your selection to a queue. The RP Slice dialog can be started in one of the following ways: Via the main toolbar:  Select the RP Slice button Via the menus: Select RP Slice from the File menu. This opens the RP Slice dialog with the chosen contour format already selected. Via the Project Management: You can open the RP Slice dialog by selection the RP slice icon in the Action list of the Mask tab. Exporting contour files RP Slice Mask or File selection In the RP slice dialog you start with the selection of one or more masks.htm 2/3/2014 . Go to Options > Licenses and fill in the correct passwords.Import Page 17 of 169 The solution developed at Materialise has been called "RP Slice".

Masks/3dd/contour files to After selecting a mask. It will act like the Windows explorer. SLC. If you have a . it will be convert placed here in a queue. Depending on the selection. SLI. start with selecting a contour file.htm 2/3/2014 . The files will be processed according to the list. Selecting the files and pressing the Remove button removes the files from the queue. Select the location where you want your support files to be placed. IGES file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. If you have a contour file for which you want to generate the support structure. press this button in order to go to the RP Slice file selection window. Output Format The possible output formats are CLI.3dd file you wish to process. To generate a support file. Description of the main areas Start from Mask Start from 3DD file Start from contour file Output directory This area displays the masks that are currently available in your project.Import Page 18 of 169 To generate a contour file. Clicking on the files in the Output Filename column allows changing the file name. 3dd file or contour file and clicking the Add button. RP Slice/STL+ to CLI. You can look at all the drives of your computer and their directory structure. different dialogs will be shown after clicking the Next button. press this button in order to go to the RP Slice file selection window. start with selecting a mask or 3dd file. When you click the button a window appears. Select here the desired mask(s) to process. SLI and SLC.

Standard the highest position will be displayed. Standard the lowest position will be displayed. it might be better to use the STL interface. you don't have to change anything here. It is also possible to build a part in two pieces with one part from top to middle and the other from end to middle. or the user wants to build it in two pieces. another time from the middle to the end. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. In this way the pieces will fit better. For the stereolithography machine. Note: It is advised to use these functions for interfacing to the RP machine whenever possible. The files are very close to machine files and contain all the vectors which will be used on the RP machine. Descending: the highest table position will be built first. If the model is too high to fit in the RP machine. If you want to build the entire mask or file. Position Last Slice This table position indicates up to where the part should be made. The highest table position will be built last. The lowest table position will be built first.htm 2/3/2014 . Position First Slice Build Direction Here you can toggle between ascending or descending: Ascending: the lowest table position will be built first. This can be interesting when building a complete skull or if one wants to avoid supports inside the skull. and in some other restricted cases. Slice Positions The table position of the image data set has to be entered. Only when no direct interface is provided. both the contours and the internal hatchings will be generated. one can process the same file twice: one time from the start to the middle.Import Page 19 of 169 This function will generate files for different Rapid Prototyping Systems. The functions provide higher order interpolation algorithms and give the most accurate and highest resolution models possible.

When the slices are 2 or more millimeters separated it is advised to use the cubic interpolation. the dashed lines show linear interpolation between 4 points of a contour. the checkbox should be marked. Choose the option "none" when there is no label. The black dots are the original contour points. a linear interpolation is in most cases good enough. Clicking the Next button will link you to the RP Slice calculation parameters page. the small vertical lines mark the interpolation distances. Linear is the default as it is faster and gives good results in cases with small slice distances. Cubic interpolation will give smoother surfaces as show in the next figure.htm 2/3/2014 . The solid line is the cubic interpolation and the dashed line shows the linear interpolation. Sometimes building the model upside down is preferred because less support is needed in this direction. Cubic Interpolation Two inter-slice interpolation schemes are implemented: Cubic and linear interpolation. In the image you see a comparison between linear interpolation and cubic interpolation. In the figure. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 20 of 169 The program will take care of mirroring. If the original images are only 1 mm separated. Labels This radio button determines whether the label will be in color (color stereolithography only) or punched. the full lines show the cubic interpolation. Color Stereolithography only If a part needs to be built in color.

Mostly this value is the half of the X hatching space. one can define the hatching space for the coloration. it is possible to create directly the vector files for the machine. This will speed up the procedure even more. Same as in X. For creation of a model with colored regions.Import Page 21 of 169 RP Slice Calculation Parameters Hatching parameters X hatching space For interfacing to a 3D systems SLA 250 (SLI files).15 mm is faster than 0. This parameter defines the distance between the hatchings on the Stereolithography machine. Slice Resolution This value determines the internal representation of the output file: the units are one over the slice resolution.25 mm. but in the Y direction.htm 2/3/2014 . Build parameters Layer thickness This parameter defines the output layer thickness in mm. For epoxy resins (Stereolithography) with a low penetration depth. If the slice resolution is 100. the values in the output file are file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Same as in X but in the Y direction. It must be chosen in function of the Rapid Prototyping machine and its material.25 mm is advised. It is a good compromise between model quality and build time. a layer thickness of 0. For having an acceptable surface quality a layer thickness of maximum 0. Y hatching distance X color hatching space Y color hatching space For other output formats this parameter has no influence.

If you encounter contours which are cut of at a certain maximum x and y value. becomes Out of Line Distance This When the distance between a point and a line – constructed by two other points – is smaller than the out of line distance.Import Page 22 of 169 1/100 mm. The first layer height gives the value of the translation according to the direction of building in mm.01 mm 535 mm 80 0. support starts at 0 mm. this point will be removed. 80 and 200 are supported. The higher the slice resolution. one of the points will be removed. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. or support starts at 6 mm. In this way support height can be chosen afterwards by choosing the start of the support (e. a higher slice resolution gives a smaller working space.1 and smaller than 100. it is possible that the slice resolution is too high.005 mm 327 mm 100 0.0125 mm 819 mm Note: on the 3D systems SLA only resolution 40. the more accurate one can work. Minimal Segment Length This When the distance between two points is smaller than the minimal segment length. On the other hand.g.htm 2/3/2014 . First layer height Scale factor Filters These parameters filter out data points of the contours in order to reduce the file size and thus the calculation time. the part at 10 mm). the part at 10 mm. This parameter allows you to rescale the original object with a factor larger than 0. Some examples : Slice Resolution Units Maximum dimensions 200 0.

ini which you can find in the installation directory. These are stored in a file called material.Import Page 23 of 169 becomes Minimal Contour length These parameters will remove contours whose length is longer than the parameters set.htm 2/3/2014 . To do this go again to RP Slice and choose to generate a file from a Contour file: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Pressing the Finish button starts the RP Slice calculation which runs in a separate program so you can continue to work in Mimics. Support Generation After the creation of a sliced file. Restoring Defaults Pressing the Restore Defaults button restores the parameter values to their original values. you can also generate a support file.

htm 2/3/2014 . You will then go to step two of the RP Slice wizard where you can choose different parameters for your support file. add the desired file and click on Next. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 24 of 169 Select the type of the Input and Output file.

the perforation will also continue on the borders of the support. (must be smaller than half the hatching distance) If this value is 0.htm 2/3/2014 . the perforation option is off Perforation Angle Nr. The same in the y-direction. The length of the straight part: distance (3) expressed in numbers of layers. When this is checked. of straight layers Perforated Borders Angle (2) in the drawing below. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 25 of 169 Hatching Parameters X Hatching Space Y Hatching Space The distance between two support walls in the x-direction. Perforation Perforation Length Distance (1) in the drawing below.

no supports will be created for the cranium. All features higher than the Ending Height will not be supported (see picture).Import Page 26 of 169 Support Angle The maximum angle which can be built without support.htm 2/3/2014 . (angle in function of the horizontal plane. All surfaces which are flatter than that angle will become supported. You can calculate the Support Ending Height by calculating the height of support via table positions in Mimics and adding the First Layer height (parameter from STL+). Be aware that the support will not go below 0 (in the z-direction). Starting Height Ending Height Instead of specifying an ending height one can also select the Full Height option. in a lot of cases. if you build a complete skull. where needed (see picture). For instance. This will force the support to be build up to the top of the part. in degrees) Starting height of the support structure (see picture). This is useful if you know that no supports are needed higher than a certain height. By putting this parameter above the orbits. no support is needed inside the skull. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

some of these parameters will be of no interest. 'Pressing the Finish button starts the RP Slice calculation which runs in a separate program so you can continue your work in Mimics. (File / Save) and clear (File / Clear) In Partman do: File / UNIX.stl s_name.  Do the normal preparation in Partman with the "s_name. restores the parameter values to their original values. RP Slice and Lightyear file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.g. Together with the sli file. Generate support for the sli file with the RP Slice program (generate also an sli file) : s_name.htm 2/3/2014 .sli" [enter] exit [enter]. STL however it is an internal 3D systems file format which is not directly supported by Partman. Copy the machine files to your SLA computer.stl): this stl file is just a box with the same dimensions as the slice (sli) file. Generate the sli file with RP Slice (e. but with extension stl (name. ranges etc.sli On the Unix prompt type : cp name.stl" as you do for normal stl files (including support settings. How to work with sli files on the 3D systems SLA 250 ? The sli files are the most direct way to make models on the SLA 250. In this way we have a stl file with the same position as our support sli slice file. But. the program will also generate a dummy stl file with the same name as the sli file. This value will determine how far the support must be separated from the part. In Partman do : File / Load (your spreadsheet file) Then prepare your parts with "Prepare" (choose "prepare" and not "prepare all") The program should tell you that the files are already sliced. name. Make sure that the x and y hatching spacing are filled in correctly.Import Page 27 of 169 If you don't want the support to damage vertical walls. And type: "touch *.stl downwards in the z-direction with the same amount as the height of the support (save it again). and build your parts. it might be interesting to use an xy-offset for the support generation. These are stored in a file called material. XY Offset Restoring Defaults Pressing the Restore Defaults button. save the spreadsheet.ini which you can find in the installation directory. there is an easy workaround to bring these files on your machine. and it will directly generate the machine files.stl" and "name.stl (depending upon your file name) In Partman you can translate the file s_name.sli). In that case they will be disabled so that the box to fill in the parameters is not accessible.…)? When you are finished. Depending on which file format you have chosen.

so we will use this format.3. 2. 4. We will use Mimics.Import Page 28 of 169 This section will give an explanation about how to make models in Mimics that can be built on 3D Systems SLA machines. To export the model to an SLC file. 3. RP Slice can export to three different sliced formats: 1.htm 2/3/2014 . The three main advantages of this approach are: 1. Support Generation: the perforated supports save material. It is far better to use the RP Slice module to make a sliced file of the model. Most of the time exporting the models to STL and then importing them in Lightyear is very difficult because of the size of the files. CLI: Common Layer Interface SLI: 3D Systems Layer Interface file SLC: 3D Systems Layer Contour file The latest version of Lightyear is only compatible with the SLC format. click on File -> RP Slice or click on the RP Slice button on the main toolbar: . are easier to clean and can be build faster (up to 4 times as fast) Note: This procedure was tested on Lightyear 1. Create a sliced file The first step in the process is making a sliced file from your model. 3. High resolution can be maintained. The model will look less stair-stepped. because it is already sliced Cubical interpolation can be applied. No Problems with big files. This will bring up following interface: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. RP Slice and Lightyear to make the link between Mimics and the SLA machine. 2.

3dd-files or Contour Files.Import Page 29 of 169 You can export sliced files from Masks. To export from a mask. When you click on the Next-button. the build direction and choose if you want to use cubic interpolation: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 . This will list the mask in the list of the files that will be converted. select a mask and click on the Add-button. Now select the SLC format as the Output format. you can adjust the slice positions. You can also change the name of the sliced file by clicking on the output file name.

Import Page 30 of 169 When you click again on the Next-button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Several other calculation parameters can be adjusted. please refer to the calculation parameters page.htm 2/3/2014 . For more information about these parameters.

Just select the 3dd tab on the first screen. please make sure the Layer Thickness of the sliced file is the same as the layer thickness that you will use in Lightyear. This will bring up following interface: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Saving sliced files from a 3dd file is done in the same way.Import Page 31 of 169 Note: To make the import process in Lightyear faster. the conversion process is started and the sliced file is saved.htm 2/3/2014 . Generate the support file To generate a support file for a sliced file. click on File -> RP Slice or click on the RP Slice button on the main toolbar: . When you then click on the Finish-button.

htm 2/3/2014 . Now select the SLC format as the Input and the Output format and then browse to the directory where you have saved your sliced file. You can then add the file with the Add-button.Import Page 32 of 169 Select the tab Contour Files. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. you can adjust several support generation parameters. please refer to the support generation page.Import Page 33 of 169 When you click on the Next-button.htm 2/3/2014 . For more information about these parameters.

0 and PLY. The number of triangles determines the quality of the reconstruction: the more triangles.Import Page 34 of 169 When you then click on the Finish-button. Both the model and the supports will then be loaded in Lightyear and can then be prepared for building on the SLA machine. VRML 2. ASCII STL. the support generation process is started and the support file is generated. Starting STL+ file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Read more about this on the STL+ calculation parameters page. the higher the quality. DXF. a triangle mesh will be generated around the selected volume. The disadvantage is that more triangles require more memory. go to File and then Open File. The STL+ module provides powerful tools to perform a significant reduction of the file size.htm 2/3/2014 . Open the files in Lightyear In Lightyear. STL+ The STL+ module provides interface options via triangulated formats: Binary STL. Select both files and click on Open. You can then browse to the directory where you have saved the sliced file and the support file. Using the STL+ module.

After completing these parameter values the files will be exported. CAD objects or FEA meshes.Import Page 35 of 169 All STL+ functions are loaded immediately in Mimics after registration of the STL+ module. Exporting triangulated files STL+ mask. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. the 3D calculation parameters dialog will appear after clicking the Next button. Remark that you are not allowed adding a combination of masks. By clicking the Add button you add your selection to a queue. When masks or 3dd files are added to the queue. you probably haven't entered the passwords yet. VRML or PLY) in the Export menu. 3dd files. 3dd files. all objects will be exported immediately after clicking the Finish button. Via Project Management: Select the action button in the mask or 3D tab and select the STL+ icon. When 3D objects. Go to Options > Licenses and fill in the correct password. When no project is opened in Mimics or when only the STL+ module is licensed (and not the Mimics basic module) you can only select a 3dd file. 3D or file selection In the STL+ dialog you start with the selection of one or more masks. ASCII STL. CAD objects and FEA meshes. All files in this queue will be exported in the selected output format and will be saved in the selected output directory.htm 2/3/2014 . CAD objects or FEA meshes are added to the queue. Note: If you're not able to start STL+. 3D objects. The STL+ dialog can be started in one of the following ways: Via the main toolbar:  Select the STL+ button Via the menus: Select STL+ from the File menu Select an STL+ output format (Binary STL. DXF. 3D objects. This opens the STL+ dialog with the chosen output format already selected.

The files will be processed according to the list.Import Page 36 of 169 Description of the main areas Start from Mask Start from 3D Start from 3dd File Start from CAD Start from FEA Output directory This area displays the masks which are currently available in your project. This area displays the FEA meshes that are currently available in your project. Select here the desired CAD object(s) to process. It will act like the Windows Explorer. ASCII STL. You can look at all the drives of your computer and their directory structure. Select here the desired mask(s) to process. The color of the objects will also be saved.3dd file you wish to process. press this button in order to go to the STL+ file selection window. VRML files can be used as input to Virtual Reality. 3D object or 3dd file and clicking the Add button it will be placed here in a queue. Output Format The possible output formats are Binary STL. PLY and single PLY file. Selecting the files and pressing the Remove button removes the files from the queue.0. Select the location where you want your triangulated files to be placed. Clicking on the files in the Output Filename column allows changing the file name.htm 2/3/2014 . Masks/3Ds/3dd files to convert After selecting a mask. Select here the desired FEA mesh(es) to process. enabling you to create file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. When exporting multiple objects to a single PLY file. DXF. Select here the desired 3D object(s) to process. This area displays the 3D objects that are currently available in your project. If you have a . Mimics will create one PLY file that contains all objects. This area displays the CAD objects that are currently available in your project. VRML 2. When you click the button a window appears.

without decreasing the resolution). STL+ . It will search for (approximately) flat surfaces in the STL file and reduce the amount of triangles to fill in these surfaces. Especially for technical CT applications (and all high resolution scan’s).g. contour interpolation is a 2D interpolation in the plane of the images that is smoothly expanded in the file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Two methods for reducing the number of triangles are available: Image matrix reduction and/or triangle reduction. Medium. Method Basically.STL / VRML Parameters The STL/VRML interface will generate a triangle mesh around the selected volume. High and Maximum settings. Quality All these quality aspects are grouped in the predefined Low. The downside is that more triangles require more memory. For medical applications the contour interpolation gives nicer results. The Custom setting is user defined. This should be considered when calculating an STL file. The method used to interpolate the images and generate the 3D triangular mesh can be chosen out of two options: grey value interpolation and contour interpolation. The number of triangles determines the quality of the reconstruction: the more triangles. for technical applications grey value interpolation is preferred A smoothing algorithm changes the overall appearance of the triangular mesh.Import Page 37 of 169 multi-color objects suitable for color 3D printing.htm 2/3/2014 . it is recommended to study the 3D generation parameters and to define practical custom settings. The Triangle reduction algorithm reduces the file size (the amount of triangles) keeping the STL surface as close as possible to the original one (e. the higher the quality.

changing the Z resolution (see below) will most likely result in a violation of this condition because the slice distance for the calculation will increase. Scaling The scaling option allows you to scale the part during export. If this factor is low (close to 0). When using contour interpolation.htm 2/3/2014 . The calculation can be reduced to a part of the segmentation by adapting the table positions. Changes of the Z resolution therefore should not be used in combination with grey value interpolation. You can also choose to use a shrinkage compensation. Triangle Reduction Triangle reduction allows you to reduce the number of triangles in the mesh. The Reset button will restore the default values.g. Note: if you take a high smooth factor. The reduction is given relative to the X-size (=Y-size) of a pixel in the image and relative to the height (Z-size) of a pixel in the 3D data set. The smooth factor indicates the importance of local geometry. The visual representation will be quite good. XY resolution Decides how many voxels are grouped in the XY plane Z resolution Decides how many voxels are grouped in the Z-direction Note: When using grey value interpolation. the table positions of the first and the last image are shown in the table. There are three Reducing modes of triangle reduction. the number of iterations should be kept low. However. It works like a filter for noise reduction. reducing too much will lead to incorrect dimensions of the object. This shrinkage compensation will make sure that the volume of the part before smoothing and after smoothing is similar. This makes it easier to manipulate the file. This way you can e. Artificial holes might appear in the 3D image but the dimensions of the object will stay quite accurate. but when measuring items they will typically appear too large. every 3D object will turn into a sphere-like object! The number of iterations defines the area of influence for smoothing. the Point-type. With high values for the ratio (close to 1). A default calculation is a calculation of the whole segmentation. Matrix reduction This option allows the grouping of voxels to calculate the triangles. If too many cycles are passed. The iteration parameters express how many cycles of the smoothing are performed. Smoothing This function is meant to make rough surfaces smoother. Grey value interpolation is a real 3D interpolation and therefore more accurate. the Edge-type and the Advanced Edge- file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. reducing too much will lead to a loss of information for thin or small objects.5). Contour interpolation is recommended to use for medical CT applications. Don’t exaggerate the number of cycles! Every iteration changes the triangulation. Secondly. First of all. easily build demo parts on a scale of 50% (value 0. it is important to realize that grey value interpolation does not always produce good results. the local geometry is considered as important and the smoothing is limited. the new position is mainly determined by the position of the other points of the triangles in the neighborhood. Grey value interpolation is recommended to use for technical CT applications. this condition should be fulfilled during the scanning (acquisition). Slices Default.Import Page 38 of 169 third dimension. grey value interpolation works fine. In this last case it is obvious that we talk about smoothing. A reduction of the XY resolution does not violate the condition. Using the shrinkage compensation will have a negative effect on the speed of the calculation. Only if slice thickness and slice distance are the same.

Therefore it is better to make the interpretations on the images in MedCAD. They all have the same parameters. The Number of Iterations is a user-set value that defines how many times the program should make the calculations. A CAD software is not an imaging software. with the anatomical data in a transparent mode. essential part information may get lost. On the menu bar: The MedCAD menu lists geometrical objects that can be drawn freely or fitted onto polylines.Import Page 39 of 169 type. It is advisable not to use the reducer on very noisy objects. Triangles deviating less than this angle will be grouped into the plane of the other triangles. The Working Buffer size relates directly to the amount of memory used to process the reduction. etc. There is no specific way to start MedCAD. When the module is registered the extra feature appear in the interface. Only the surfaces which are needed to make a fit are really converted to B-spline surfaces. The Tolerance indicates the maximum deviation in mm that a related triangle may have. More iterations therefore do not make a lot of sense. anatomical landmarks). The point reduction and the edge reduction are better for technical objects since they create more uniform meshes. MedCAD MedCAD is designed to make a bridge between medical imaging (CT and MR) and CAD design. The algorithm needs several iterations to reduce the number of triangles in larger flat areas. to be part of the same plane that contains the selected triangle. The higher the buffer size. If a plane. taking into account all the gray value information (soft tissue. On the images. It makes sense to keep this value related to the pixel size (e. MedCAD is not a design software. On the other hand. If you try to convert all the medical data to your CAD system. tendons.…). defined by the Tolerance and the Angle consists out of several triangles. different types of bone. It also allows you to file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Learning yet another CAD system would be a waste of time. The Edge-type will remove a triangles edge (two points + the connecting line between these two points). the greater the part of the segmentation that can be calculated at once. The Point-type reduction mode will try to reduce the amount of triangles by removing a point. Not all the data from the images can be converted to the CAD system: only a surface representation of the images is visible in the CAD system. With this method. or in 3D shaded representations. The Edge Angle-value defines which angle should be used to determine edges of the part that cannot be removed. If the tolerance-value is too big. Many software packages are available to make designs and most designers are already familiar with a certain CAD package. This means that it can export data from the imaging system to the CAD system and vice versa. Starting MedCAD All MedCAD functions are loaded immediately in Mimics after registration of the MedCAD module. Use the right tools in the right software. This algorithm converges to a stable result after about 15 iterations. CAD design can be imported in the Mimics via the STL interface. basic features can be recognized and converted to geometrical entities (basic axes. half the pixelsize or a quarter). the program will try to retriangulate this area. your system will slow down drastically. In this case it is better to perform a smoothing first. reference curves. The designs are visualized in 2D sections together with the actual images. it is possible to bridge between the images and the CAD system in a few minutes time.htm 2/3/2014 . The advanced edge reduction algorithm generates less noise on the resulting surface and creates a smaller object.g.

Go to Options > Licenses and fill in the correct passwords. Lists if the object is visible or not by means of glasses. In the Project Management: Extra CAD Objects tab page. Note: If you're not able to start MedCAD. By clicking on the name of the object. Extra options are added to the action list of the Polylines tab : select a polyline-set and click on the action button to fit a MedCAD object on the polylines or to export the polylines as Iges. you probably haven't entered the passwords yet. CAD Objects tab List of created Objects Name Visible Name of the object.htm 2/3/2014 . it can be renamed.Import Page 40 of 169 fit freeform curves and surfaces on polylines. In the Export menu: Two new export file formats are added: Point Cloud and Iges. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

The entities used are of type 106 and form 12 (linear path entity). Exporting Iges files Different Iges export possibilities are available in MedCAD: Starting from the Export menu: By selecting Iges in the Export menu. Note: If you only want the contours of the mask. If you want to maintain the original position in space. Locates the selected MedCAD object The action button lists all the available action on MedCAD objects. Displays the properties of the selected object. The advantage of starting the Iges export from a mask is that you can create extra contours (inter-layer) due to interpolation (see the “layer thickness” parameter on the RP Slice calculation parameters page). make sure the First Layer height parameter is set to the first table position.Import Page 41 of 169 Functions on Objects New Creates a new Object.htm 2/3/2014 . (Otherwise the contours will be translated to this value) Starting from the Polylines tab page: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. a dialog is displayed where you can choose to export the contours of a mask or a 3dd file as an Iges file. make sure the “layer thickness” parameter is set to the slice distance of the image set. The disadvantage is that all contours of your mask will be exported. Although. there are filters available to filter out small contours and data points of contours in order to reduce the file size. Delete Properties Locate Action Deletes the selected objects. The object menu appears : Click on the desired object to go to the correct help page. You can generate a mask from a MedCAD object or export them as IGES (International Graphics Exchange Standard) or as STL.

line. The entities used are:   Analytical Geometrical objects (sphere. The same filters are available as in the RP Slice module. Surfaces): NURBS representation.htm 2/3/2014 . Description of the main areas Select a 3D to export in This area displays the 3D objects that are currently available in your project. all available CAD objects in the project are exported as one Iges file. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. If you want separate Iges files for each CAD object. For example. a dialog is displayed where you can choose to export a 3D object as a Point Cloud file. …): according the standard IGES representation. a sphere is exported as a circular arc revolved around an axis. the selected polyline set is exported as an Iges file. Starting from the CAD Objects tab page: By selecting one or more CAD objects in the CAD Objects tab page of the Project management and by clicking the Iges Export button.Import Page 42 of 169 By selecting a polylines set in the Polylines tab page of the Project management and by clicking the Iges Export button. plane. The advantage of starting the Iges export from a polyline set is that only the contours of interest are exported. Starting from MedCAD menu: By selecting Export all Objects to Iges in the MedCAD menu. The disadvantage is that interpolation between the contours (interlayer) is not possible. Free form objects (Curves. the selected CAD Objects are exported as one Iges file. use the Iges Export button in the CAD Objects tab page of the Project Management. Exporting point cloud files By selecting Point Cloud in the Export menu. The entities used are of type 106 and form 12 (linear path entity).

Correlation A measure for the strength of matching (%). If it is turned off only the current polyline will be grown.htm 2/3/2014 . File name Save as type MedCAD Menu MedCAD Menu This menu contains the following items: Polyline Growing Starts the Polyline Growing mode. The parameters needed are: From To The set from where the polylines are grown The set to where the polylines are grown to. The operation can be performed on one single polyline or in 3D. This is done with a geometrical comparison. It will act like the Windows Explorer. This can be an existing selection or a new created one. You can change the file name of your Point Cloud file. The Polyline Selector Toolbar appears: The Polyline Growing tool provides the capacity to create several sets of polylines. If this parameter is turned on.Import Page 43 of 169 Point Cloud format Output directory Select here the desired object to process. When you click the button a window appears. Keep Originals By default the polyline that is grown into a new set is removed from the source set. You can choose to keep this polyline in the source set by enabling the Keep Originals checkbox. Selection is done on the images in 2D by drawing a rectangle (Press the left mouse button to indicate a corner of file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Auto multi-select This parameter can be turned on/off. At this time the only possible output format is Ascii. all polylines according the Matching parameter will be grown. You can look at all the drives of your computer and their directory structure. Select the location where you want your Point Cloud file to be placed.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. If there is a polyline where the shape is a bit deformed. you can alter it by editing on your segmentation mask. and Z coordinates of the point. Keyboard The following window appears: Type in the X. drag and release to indicate the opposite corner) around the desired polyline. Y.htm 2/3/2014 . Simply click on the 2D images to create a point. The point can be moved in the 2D images and 3D view by dragging it with the left mouse button. Point Creating Points There are two ways to create a point: Draw The cursor will change to . In the edit mode you will be able to update the polylines.Import Page 44 of 169 the zoom rectangle.

Opens the CAD Objects tab page in the Project Management. Draw The cursor will change to . Simply click a start and end point on the 2D images to create a line (Start and end point can lie in different images) The line can be moved in the 2D images by dragging the end points with the left mouse button.htm 2/3/2014 . Context menu Delete Hide CAD Objects List Deletes the selected point.Import Page 45 of 169 Click on the colored button in order to change the color of the MedCAD object. Line There are three ways to create a Line: Fit on Polylines When creating an object based on a polyline set. Hides the selected point. the following window appears: Select the desired polyline set to fit the object on and press OK. Keyboard file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

and Z coordinates of the start and end point of the line.Import Page 46 of 169 The following window appears: Type in the X. the following window appears: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Y. Context menu Delete Hide CAD Objects List Deletes the selected line. Opens the Objects tab page in the Project Management. Hides the selected line. Circle There are three ways to create a circle: Fit on Polylines When creating an object based on a polyline set. Click on the colored button in order to change the color of the MedCAD object.htm 2/3/2014 .

The circle can be moved in the 2D images by dragging its center point with the left mouse button. Click on the colored button in order to change the color of the MedCAD object. Y. followed by the direction: the coordinates of the direction of the normal vector of the plane in which the circle is located. Entering the radius fully determines the circle (see figure). Draw The cursor will change to . and Z coordinates of the center point. Keyboard The following window appears: Type in the X. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Changing to another slice or to another 2D window is possible.htm 2/3/2014 .Import Page 47 of 169 Select the desired polyline set to fit the object on and press OK. Simply click three points on the 2D images to create a circle.

Sphere There are three ways to create a Sphere: Fit on Polylines When creating an object based on a polyline set. Draw file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. the following window appears: Select the desired polyline set to fit the object on and press OK. Hides the selected circle.htm 2/3/2014 .Import Page 48 of 169 Context menu Delete Hide Deletes the selected circle.

htm 2/3/2014 . Plane There are three ways to create a Plane: Fit on Polylines When creating an object based on a polyline set. Y.Import Page 49 of 169 The cursor will change to . The sphere can be moved in the 2D images by dragging the control points with the left mouse button. Context menu Delete Hide CAD Objects List Deletes the selected sphere. and Z coordinates of the center point and the radius. Hides the selected sphere. Opens the Objects tab page in the Project Management. Changing to another slice or to another 2D window is possible. the following window appears: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Click on the colored button in order to change the color of the MedCAD object. Keyboard The following window appears: Type in the X. Simply click four points on the 2D images to create a sphere.

Change the width and height of the plane to change the visualization in the 3D view of the plane.Import Page 50 of 169 Select the desired polyline set to fit the object on and press OK.htm 2/3/2014 . Keyboard The following window appears: Type in the X. Simply click three points on the 2D images to create a plane. Draw The cursor will change to . and Z coordinates of a point which is part of the plane followed by the coordinates of the normal vector of the plane. Context menu file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The plane can be moved in the 2D images by dragging the control points with the left mouse button. Y. Click on the colored button in order to change the color of the MedCAD object.

htm 2/3/2014 . Hides the selected plane.Import Page 51 of 169 Delete Hide CAD Objects List Deletes the selected plane. the following window appears: Select the desired polyline set to fit the object on and press OK. The cylinder can be moved and in the 2D images by dragging the control points with the left mouse button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Opens the Objects tab page in the Project Management. Simply click a start and end point of the cylinder axis. Draw The cursor will change to . Cylinder There are three ways to create a cylinder: Fit on Polylines When creating an object based on a polyline set. followed by a point which indicates the radius on the 2D images to create a cylinder (see figure).

Click on the colored button in order to change the color of the MedCAD object.htm 2/3/2014 .Import Page 52 of 169 Keyboard The following window appears: Type in the X. followed by the radius of the cylinder. and Z coordinates of the start and end point of the cylinder axis. Hides the selected cylinder. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Context menu Delete Hide Deletes the selected cylinder. Y.

Some caution in increasing the number of control points is advised. Draw When Draw Curve is selected the cursor changes to . Properties file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Best values are either 3 or 4. This area (under the Polyline Set selection) indicates if the polyline set is valid for freeform curve generation. The order of the polynomials used. The more control points used.Import Page 53 of 169 Freeform Curves There are two ways to create a Freeform Curve: Fit On Polylines Polyline Set Set Check Order Number of control points Closed Select the desired polyline set.g. The curve can be moved in the 2D images by dragging the control points with the left mouse button.htm 2/3/2014 . the better the fit will be. if the number of points is too high. an order of 3 means that cubical polynomials are used. So. the fit of the polyline will become worse. The curve can be closed or not. Left click on the images where the curve has to pass through. The basis of a B-spline is a polynomial and a polynomial has the tendency to wave. e. Control points can be seen like little magnets which attract the curve. double click to end the curve.

You can also find some information about the order and the control points of the curve. CAD Objects tab. The following window appears: Polyline Set Set Check Select the desired polyline set.htm 2/3/2014 . Here you can change the color and the name of the curve. This area (under the Polyline Set selection) indicates if the polyline set is valid for file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Freeform Surfaces The only way to create a freeform surface is to fit it on a polyline set.Import Page 54 of 169 You can view the properties of a Freeform Curve by clicking on the Properties button in the Project Management.

The order of the polynomials used. These centerlines can be exported together with a range of measurements. The v-parameter runs in the image plane. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Freeform Surface Info You can view the properties of a Freeform Surface by clicking on the Properties button in the Project Management. the better the fit will be. For each parameter Order. Some caution in increasing the number of control points is advised.htm 2/3/2014 . The more control points used. Freeform Tree This tool allows you to calculate the centerline of a 3D object. These are the running coordinates in two in-plane orthogonal directions. Here you can change the color and the name of the surface. In MedCAD those two plane-directions are fixed.Import Page 55 of 169 Order Number of control points Closed U en V parameters surface generation. The u-parameter runs perpendicular to the image plane. the fit of the polyline will become worse. A parametric surface typically has 2 parameters: a u-parameter and a v-parameter. The surface can be closed or not. The basis of a B-spline is a polynomial and a polynomial has the tendency to wave.. but a torus. if the number of points is too high. You can also find some information about the order and the control points of the surface. Caution: a surface closed in two directions is NOT a cylinder closed on top and bottom. Best values are either 3 or 4. e. Number of control points and Closed have to be set. CAD Objects tab. So. an order of 3 means that cubical polynomials are used.g. Control points can be seen like little magnets which attract the surface.

Number of iterations Set the amount of iterations you want the algorithm to perform. Distance between control points Set the distance between two successive control points Freeform tree properties file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 56 of 169 Resolving resolution Select the minimum detail you want to resolve.htm 2/3/2014 .

htm 2/3/2014 . Select a branch and click on delete to remove the branch from the list.Import Page 57 of 169 Label Name Visualisation Color Name of the centerline Sets the color of the centerline The name of the branch Length of the branch The visibility of a branch can be toggled by clicking on the sunglasses. You can export the centerlines as Iges files or export the coordinates of the centerlines and the measurements Branches Name Length(mm) Visibility Delete Export file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

Diameter of the subscribing circle in a control point.. the normal are represented as Nx. minimal and maximal diameter can be exported as an Iges file. Measurment Best fitted diameter Minimal diameter Diameter of the best fit circle in a control point.htm 2/3/2014 . Besides the control points also the best fitted. Py and Pz. The measurement is exported as Maximal diameter file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The measurement is exported as Dmin. Export of centerline Properties Export Output Directory File Name Save as type Select the destination folder. The information is grouped per branch and is listed in columns. the coordinates of the control points are indicated by Px. Diameter of the inscribing circle in a control point. The text file will list the position and measurement information of the control points. Select the file name The centerlines can be exported as Text or as Iges file.Import Page 58 of 169 on the centerlines as Text file. Ny and Nz. The Iges file exports the control points and the connection between them. The measurement is exported as Dfit.

. use the IGES button in Project Management. the normals are indicated by Ncx. The Hydraulic ratio is exported as Xh. If however you want to created separate IGES files for every object. the volume mesh can be imported in Mimics again. Starting the FEA module All FEA functions are loaded immediately in Mimics after registration of the FEA module. You can calculate 3D objects based on the scanned images and prepare these surface meshes for Finite Element Analysis purposes.htm 2/3/2014 . CAD Objects Tab.. Patran neutral. The coordinates of the curvature point are exported as Pcx. Pcz." is selected. Materials can then be assigned to the volume mesh. The Hydraulic diameter is exported as Dh.Import Page 59 of 169 Curvature Tortuosity Hydraulic Diameter Hydraulic Ratio Dmax. In the Export menu.. When the module is registered. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. all created objects (spheres. This is the point of the circle that determines the curvature for the segment that has a length as indicated in the measurement interface and has the control point as a mid-point. FEA The Mimics FEA Module enables you to link from scanned images to Finite Element Analysis (FEA) and Computational Fluid Dynamics (CFD) by exporting the files in the appropriate file format. In the Project Management: Extra FEA Mesh tab. a few extra items are visible in the interface: On the menu bar: An extra FEA menu. Ncy. The coordinate and normal of the curvature point. based on the Hounsfield Units in the scanned images or on the segmentation of the project. Fluent and Nastran..) will be exported to one iges file. Hydraulic diameter in each control point. The Remesher in the FEA Module assures that you'll end up with the most optimal input for the pre-processor of your FEA software. The name of this file can be given in the dialog box that will be displayed.. Export all object to IGES When "Export all objects to IGES . Hydraulic ratio in a control point. freeform surfaces. listing the different FEA functions. new export file formats are added: Abaqus. Ncz and the radius that defines the curvature is represented by Rc. Pcy. After converting the surface mesh to a volume mesh in the pre-processor. Ansys.The Tortuosity is exported as T. Tortuosity of the segment that has a length as indicated in the measurement interface and the control point as a mid-point.

By clicking on the name of the object. Note: If you haven't assigned any materials to a FEA mesh. it can be renamed. Go to Options > Licenses and fill in the correct passwords. Lists if the material assignment is visible or not by means of glasses. you will not be able to make the material assignment visible. You can change the visibility by clicking on the glasses. You can display or hide the contours by clicking on the glasses. Lists if the object is visible or not by means of glasses.Import Page 60 of 169 Extra buttons on the 3D Objects tab and the STLs tab: select a 3D Object or STL and click on the Remesh button to open the remesher with the part already opened.htm 2/3/2014 . You can display or hide the material assignment by clicking on the glasses. FEA Mesh tab List of created Objects Name Visible Material Name of the object. Note: If you're not able to start the FEA module. Contour Visible Lists if the contours of the volume mesh are visible in the 2D images or not by means of glasses. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. you probably haven't entered the passwords yet.

For more information about the import process. Displays the properties of the selected object: Material Export Calls the window to do a material assignment for the selected object. This menu lists the different features of the FEA module: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 61 of 169 Functions on Objects Import Delete Properties Imports a volumetric mesh.htm 2/3/2014 . the FEA menu appears in the menubar. Deletes the selected objects. Ansys. FEA Menu FEA menu When the FEA module is licensed. Abaqus or Fluent file. Exports the selected object to a Patran neutral. please refer to the Import help page.

the volumetric mesh will be loaded and listed in the FEA mesh tab. Ansys and Abaqus volumetric meshes. If you choose yes. You can import Patran neutral. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. For more information about which elements are supported please read the Supported Files page.htm 2/3/2014 . When you click on the Ok button. the remesher will automatically be started with the selected object already loaded. You can select exactly one 3D object or STL out of the list. When you close the remesher.Import Page 62 of 169 Remesh Allows you to select a 3D object or an STL that will be remeshed. the selected 3D or STL will be replaced in Mimics by the remeshed part. you will be asked if you want to save the changes or not. Import Allows you to browse for a volumetric mesh. When you have selected the right file and click on the Open button.

Ansys. both the mesh and the material assignment (if available) will be exported. When you have selected the correct mesh and click on the Ok button.Import Page 63 of 169 Material Allows you to select a FEA mesh out of the list for which you want to assign materials. Export Allows you to export a 3D object. a STL or a FEA mesh to a Patran Neutral. Fluent or Nastran file.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. the material assignment window will be opened for the selected mesh. Abaqus. In the case of a FEA mesh.

the original STL file file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. If you have altered the object. You can use the Fill Cavity from Polyline tool to remove holes from your 3D object. you can do a shell reduction so that small shells are removed. It is also interesting to fill as much holes as possible. close the remesher.Import Page 64 of 169 Note: FEA meshes can also be exported to a colored STL file.   Note: When you are remeshing an object. Most FEA packages don't like small details. These colored STL files are invalid STL files and should only be used for visualization purposes! The colored STL file could for instance be used to view the material assignment inside the volumetric mesh. the remesher will ask you if you want to save your changes. This is needed in order to raise the quality of the triangles so that the preprocessor of an FEA package can build a tetrahedron mesh from them. Note: If you remesh a STL and choose to save the temporary file when returning to Mimics. If you go to the Segmentation Menu and choose Calculate 3D and then Options. you cannot switch to Mimics. you will return to Mimics and your object will be replaced with the remeshed object. To return to Mimics. There are some steps you can do to make sure that your 3D object that is calculated in Mimics to make sure that the remeshing will go smoothly:  When calculating a 3D in Mimics.htm 2/3/2014 . If you choose yes. Thanks to the morphology operation in Mimics. In that dialog you can choose to do a Shell reduction with value 1. Remeshing A STL or 3D object can be remeshed using the remesh module. you can already smooth out small details on the surface.

In the quality histogram. These are the steps that are normally taken to make sure the mesh is optimal for FEA purposes. You can filter them out with the small triangles filter .3 to 0. You can do this step based on intuition or on the feedback from the created volume mesh quality from your FEA-preprocessor. STEP H: If low-quality triangles still persist. Stop when both the mesh looks uniform enough and the total number of triangles is small enough.and edge-based reduction decreases the number of triangles even further.htm 2/3/2014 . but an example of the application of this protocol can be found in Tutorial Case 8. STEP B: Start with normal triangle reduction with a large angle value. activate the inspection parameter and check the mean value of the smallest edge length! Do exactly the same for the largest edge length.Import Page 65 of 169 that you have loaded will NOT be changed. Remember or write down these values. First select the desired quality parameter from the quality metric dropdown box. With the SplitBased automatic remeshing a quality threshold of 0. If the volume file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Therefore it can be easier to return to Mimics and make the changes in the mask. STEP K: If small triangles persist and you do not want to increase the geometric error any further. The different parameters for each step are dependant on each dataset and won't be given in this basic protocol. STEP M: If needed you can control the growth of your triangles with the Smooth Size Transition tool. STEP L: Check and remove sharp geometry using the sharp geometry measures (sharp geometry. STEP N: If steps G. STEP A: Check if the 3D object doesn’t have thin walls or structures that will be hard to model but are of no importance for your FE Analysis. STEP C: Check the size of the triangles. Therefore select from the inspection dropdown box smallest edge length. Remeshing Protocol Below you can find a basic remeshing protocol. shafts). select a min and max edge length that do not differ more then a factor 5. the resulting 3D object may include too much detail. STEP J: Call the self-intersection test and fix them by deleting the appropriate triangles and filling the resulting hole. They are usually removed by another call to the split-based algorithm (with larger geometric error as before). The min edge length should be around the mean value of the smallest edge length inspection parameter STEP F: You can now reduce the amount of triangles preserving the achieved quality with the Quality preserving triangle reduction . use local operations to fix them. use the grouping around 'smallest edge length' to collapse them manually. STEP O: Go on to your preprocessor to generate the volume mesh and to the real FEA-analysis. peaks. Typically for FE analysis the Height/Based (N) parameter is used. Only the STL file that is saved in your Mimics project is altered. STEP D: When you notice in the inspection diagram that there are still too much small triangles.4 can be achieved. To make sure to attain this result. H and/or I introduced low-quality triangles call the split-based algorithm again. for CFD the Skewness (N) parameter is used. Removing these structures in the remesher is possible but can be time consuming. STEP I: Make the mesh more uniform by doing several calls to the quality-preserving triangle reduction with increasing geometric error. Sometimes iterating between point. STEP E: After you’ve reduced the amount of triangles you can optimize your mesh with the Split-based automatic remeshing . STEP B: Depending on the parameters you’ve selected for 3D calculation. As a first step you can do a defeaturing on the 3D object therefore select the smoothing button. STEP G: In some cases there are still some low-quality triangles left at this point (you should not have started any local operations already).

The quality measurements are based on the properties that describe a triangle: base. The magnitude of the smallest angle of a triangle lies between 0 and 60. It is a dimensionless unit that lies between 0 and 1. Smallest angle (Normalized) The normalized smallest angle parameter equals the smallest angle of a triangle. Quality Quality of the mesh There are different ways to express the quality of a mesh. This is also a dimensionless unit that lies between 0 and 1. so the minimum value is 0. All parameters can be used to be optimized in the automatic remesh operations R-in/R-out (Normalized) This parameter is the ratio of twice the radius of the inscribed circle to the radius of the ascribed circle of the triangle. angle magnitude. Largest angle (Normalized) = (180 . with 1 representing an equilateral triangle.Largest Angle)/120.Import Page 66 of 169 mesh is inadequate return to step I. It is a dimensionless unit that lies between 0 and 1. Edge ratio (Normalized) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 . As base the largest edge is taken. ascribed circle. It is not normalized. Skewness (Normalized) The skewness of a triangle is defined as the ratio of its area and the area of an equilateral triangle with the same ascribed circle. The value is normalized with the factor 2 so that for an equilateral triangle it is equal to 1. Largest angle (Normalized) The normalized largest angle parameter is a scaled value of the largest angle. Height/Base (Absolute) This parameter is the ratio of the height of the triangle and the length of its base. They all relate to the form of the triangles that constitute the mesh. length. The value lies between 0 and 1. The value is normalized with the factor sin 60 so that for an equilateral triangle it is equal to 1. For an equilateral triangle this value is equal to 1. which is positioned under the main menubar. so that its value lies between 0 and 1. so that its value lies between 0 and 1. and the maximum value (for an equilateral triangle) is sin 60 . A perfect mesh would consist of triangles that are all equilateral (each side has the same length and the 3 angles are 60 degrees). Height/Base (Normalized) This parameter is the ratio of the height of the triangle and the length of its base multiplied with sin 60 . divided by 60. inscribed circle. Smallest angle (Absolute) This parameter classifies the triangles based on their smallest angle. Quality parameters You select the quality measure you would like to use to evaluate the mesh quality of the part in the drop down menu in the iconbar. height. Angle ratio (Normalized) The angle ratio is defined as the ratio of the smallest angle to the largest angle.

or you probably want to check your mesh for sharp geometry (sharp.Import Page 67 of 169 The edge ratio is defined as the ratio of the length of the smallest edge to the length of the largest edge. Non-manifold edge (Normalized) This measure will detect when triangles have more than one neighbor over one edge. The parameters below are used to inspect the mesh. the following parameters are useful. all triangles will have quality measure 1. but slightly different than the quality parameters above.67 (triangle has one bad edge) Bad edge = 0. The height of a triangle can be 0 till any number. The largest angle of a triangle is always bigger than or equal to 60 and smaller than 180. It is not possible to do autormeshing with one of the following parameters as optimization criterion. The length of smallest edge can be 0 till any number. The value lies between o and 1. This inspection can be very diverse. It can be useful to get an idea of the size of the triangles in the mesh (largest edge length). the normal is compared with the normals of the neighboring triangles. For each triangle.33 (triangle has 2 bad edges) Surface smoothness (Normalized) This measure expresses the smoothness of the geometry. For different applications. Largest edge length (Absolute) This parameter classifies the triangles based on their largest edge length. Bad Edge (Normalized) A bad edge of a triangle is an edge of the triangle that has no triangle neighbor on this edge. If there are no bad edges. When the normals are similar. The length of the largest edge can be 0 till any number. Largest angle (Absolute) This parameter classifies the triangles based on their largest angle. shaft). Peak (Normalized) A peak is in fact a special case of a sharp geometry. Height (Absolute) This parameter classifies the triangles based on their height. or you want to look for the bad edges in the mesh. In order to be able to group bad edges. peak. you need to set the maximum quality measure to less than 1.htm 2/3/2014 . It is used to group bad edges and easily identify problem areas. for triangles on edges or where the angle with neighboring triangles is large. Equi-angle skewness (Normalized) The equi-angle skewness of a triangle is defined as the minimum of the values (smallest angle/60) and (180-the largest angle)/(180-60) Stretch (normalized) The stretch is defined as (radius of the inscribed circle/longest edge length) * square root (12). only sharp geometry of which the normals of the file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. With Peaks. the result is closer to 0. computed perpendicular on the longest edge. In fact. the result is close to 1. Smallest edge length (Absolute) This parameter classifies the triangles based on their smallest edge length. Inspection parameters The inspection parameters are also related to the quality of the mesh. the quality measure a triangle for Bad edge can only have three discrete values: Bad edge = 1 (triangle has no bad edges) Bad edge = 0.

Sharp geometry (Normalized) This measure is intended to detect sharp edges in the geometry. A sketch is given below. the geometry is concave. peaks and shaft in the following table. the geometry is convex. the triangle is actually a peak. see below) the material or pointing outwards (peak.htm 2/3/2014 . In other words. see below) the material. In this case. the shaft is defined to be 1. Shaft (Normalized) A shaft is also a special case of a sharp geometry. but when the normals are pointing towards each other. The definition is as follows: Sharp geometry = 1 – angle/180 degrees. comprises peaks and shafts AND Peak = 1-angle/180 ONLY = 1. the triangle is a shaft. are considered. but when the normals are pointing away from each other. the peak is defined to be 1. where angle can range between 0 and 180 degrees. In this case. The sharp geometry will detect both types of sharp edges. Type Sharp Definition =1-angle/180 Image Always. In other words. The definition is identical to sharp geometry. These sharp rims can be pointing inwards (shaft. The definition is identical to sharp geometry. when normals point towards each other Shaft =1-angle/180 ONLY file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. A shaft is a sharp geometry of which the normals of the triangles are pointing towards each other. We can resume the definitions of sharp geometry.Import Page 68 of 169 triangles are pointing away from each other.

It is up to the user to determine if the geometry is good enough or whether it needs to be altered. Ring-2 means that we look one level further. When tetra elements are to be constructed from the triangle data. Marked (Normalized) The mark measure will indicate marked triangles. This will create tetra elements with very poor quality. peaks can cause a problem. after a self intersection test) Growth Parameters The growth parameters focus on yet another property of the mesh: its growth. the size of this triangle is compared with the actual triangle. we created the ring definition. the growth value is 1. We use two kinds of size definitions:   Surface area Largest edge length The comparison happens in two steps. This can be sudden or very smooth. We could also express this mathematically: Which triangles are considered to be neighbors? To determine the neighbors. each triangle is compared in size with its neighbors. are considered neighbors. First of all. To express this growth. If the smallest neighbor is still larger than the actual triangle. the sharp geometry inspection measures allow a fast check of the geometry.e. If the peak is too sharp. So. the smallest neighbor is selected from all the neighbors of the actual triangle.htm 2/3/2014 . In the other case. Mainly for creating 3D meshes. With growth we mean the transition from small to larger triangles. Next.Import Page 69 of 169 =1 when normals point away from each other Why can it be useful to split sharp geometry up in peaks and shafts? It can have importance when a volume mesh is generated from the surface mesh. which are immediately connected through either a point or an edge. This problem is less severe for shafts. the growth factor is the fraction of the small neighbor and the actual triangle. This means that the actual triangle is smaller than all of its neighbors. the surface mesh shouldn’t have sudden transitions from small to larger triangles. In any case. Ring-1 means that all triangles. Ring-2 means that all immediate neighbors and their neighbors file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. the tetra element will be “squeezed” into the peak geometry. The value for a triangle is either 1 (unmarked) or zero (marked). The marked measure can be used to easily find small groups of marked triangles (i.

The following figures illustrate the definitions. Ring-3 is the same as ring 2. Part Quality Sheet (Quality histogram) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. you can find more information about how we can create meshes respecting certain growth parameters.htm 2/3/2014 . but includes the point and edge neighbors of ring-2.Import Page 70 of 169 are considered to be neighbors of the original triangle. In the section on automatic remeshing.

0 1 0 1 0 1 0 1 0 1 0 1 0 1 Left Right file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. the corresponding quality histogram will be visualized. The quality measure parameter value is presented along the horizontal axis.Import Page 71 of 169 Menu: View/ Part Quality sheet Icon: The histogram shows the quality distribution of the triangles.htm 2/3/2014 . 1 1 1 60 1 1 1 1 Left Right 60 180 Smallest height of all triangles of Largest height of all triangles of the part the part Smallest ‘smallest edge length’ of Largest ‘smallest edge length’ of all triangles of the part all triangles of the part Smallest ‘Largest edge lenghth’ Largest ‘Largest edge lenghth’ of of all triangles of the part. On the top of the histogram. By clicking one of the buttons. Quality parameter R-in/R-out (Normalized) Height/Base (Normalized) Height/Base (Absolute) Skewness (Normalized) Smallest angle (Normalized) Largest Angle (Normalized) Smallest angle (Absolute) Angle Ratio (Normalized) Edge Ratio (Normalized) Equi-angle skewness (Normalized) Stretch (Normalized) Inspection parameter Largest Angle (absolute) Height (Absolute) Smallest edge length (Absolute) Largest edge length (Absolute) Bad Edge (Normalized) Surface smoothness (Normalized) Non-manifold edge (normalized) Peak (Normalized) Shaft (Normalized) Sharp Geometry (Normalized) Marked (normalized) Growth parameter Left 0 0 0 0 0 0 0 0 0 0 0 Right 1 1 sin 60 . all triangles of the part.G. The values presented along the horizontal axis change according to the parameter selected. The histogram will look different depending on the quality parameter you have selected.I. They represent the dropdown lists in the middle of the toolbar. three buttons are shown: Q. You can choose which quality measure parameter you like to use by selecting it in the drop down menu.

You can ease the search by doing a grouping operation. Their amount is shown in the right field below the histogram. The corresponding color is green. Between minimum and maximum: The triangles with a quality measurement parameter value that lies between the minimum and the maximum threshold are considered to be of medium quality. You can fill in a value in the fields for these two parameters or you can slide the red bar (at the left of the histogram) and the green bar (at the right of the histogram).htm 2/3/2014 . The corresponding color is red. together with the percentage they constitute of the total amount of triangles. Maximum threshold: The triangles that have a quality measure value above this threshold are considered to be of high quality. Automatic remesh operations are only possible on the parameters in the dropdown list next ot the Q and G letter. The triangles that have a quality measure value above the maximum threshold will keep the part color.1-ring 0 1 Area-growth-2-ring 0 1 Area-growth-3-ring 0 1 Edge-growth-1-ring 0 1 Edge-growth-2-ring 0 1 Edge-growth-3-ring 0 1 Values at the left of the horizontal axis reflect a low quality (red color). together with the percentage they constitute of the total amount of triangles of the part. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The I parameters are used for mesh inspection purposes. The part will be divided in groups that will consist out of a number of triangles.Import Page 72 of 169 Area-growth. You determine yourself what you consider as low: when the value of the selected quality parameter of the triangle is below the maximum threshold. Their amount is shown in the left field below the histogram. The corresponding values will then be filled in the fields. and for example fix them manually. you can search afterwards for the triangles that still have a low quality. Minimum and Maximum Threshold Minimum threshold: The triangles that have a quality parameter measure value below this threshold are considered as having a low quality.). the ones with the highest quality green. Visualization Color Triangles with Low Quality Also Menubar: Tools/Quality visualization/Color bad triangles You can color the triangles that have a quality measure value below the maximum threshold. values at the right reflect a high quality (green).g. A group will contain at least one triangle that has a low quality. The colors of the triangles correspond to the colors of the bars in the histogram. Their corresponding color goes from red (low value of the quality parameter) to green (high value of the quality parameter). Their amount is shown in the field in the middle below the histogram. Group Also: Menubar: Quality visualization/Group bad triangles When there are only a few low quality triangles left (e. The triangles with the lowest quality are colored red. together with the percentage they constitute of the total amount of triangles of the part. after you have done an automatic remeshing.

if grouping is not enabled. When the boundary level is one. they will be merged to one group. the functionality is completely similar. the program shows the wireframe of the whole part when you visualize one group. the triangles that have a common edge or common corner point with the low quality triangle are added to the group. To unmark all triangles (visible and invisible) click on Unmark in the marking toolbar. a new layer of triangles is added to the group of the low quality triangle. When the boundary level is two. In case you only want to mark triangles of a certain group.5 file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. grouping needs to be enabled before mark group is possible. triangles adjacent to the bad quality triangle are added to the group. You can also show all groups by marking the checkbox. Remark: There is a limit on the quality the meshing can get: Inspection method R-in/R-out (Normalized) Height/Base (Normalized) Height/Base (Absolute) Skewness (Normalized) Smallest angle (Normalized) Largest Angle (Normalized) Smallest angle (Absolute) Angle Ratio (Normalized) Edge Ratio (Normalized) Maximum reachable Maximum threshold value 0. The amount of groups created depends thus on the amount of low quality triangles (determined by the Maximum threshold) and the boundary level.4 0. It is advised to switch to the other renderer modes when you group.25 0. When there is more than one group.> Mark Triangles -> Mark bad triangles. or marking the entire group. Determine a quality measure parameter (in the scroll down menu) Determine a maximum threshold Determine a boundary level: The grouping algorithm searches for a low quality triangle. So before you do the grouping: 1.3 0. Remark: When the renderer (Menubar/ Settings/ Preferences/ Visualization/ Colors/ Renderer) you work in is ‘software’. Obviously. etc. the entire part is visible. 4. click on the button calculate. and you would like to do a regrouping. sharp geometry.45 0. When the groups of two low quality triangles have a common triangle or common edges.Import Page 73 of 169 the triangle is viewed has having a bad quality. There are two marking options: marking the bad triangles. These buttons will always mark whatever is visible. For instance. so that the resulting triangles all have a quality parameter value above the Maximum threshold.4 0.htm 2/3/2014 . marked triangles. and will be accounted for in the grouping. The rest of the triangles are hidden and will not be marked. When you change the quality parameter.55 0. Automatic remeshing The automatic remesh module will remesh the part. you can scroll through the groups with the help of the scroll bar. not only the quality parameters.55 0. the maximum threshold or the boundary level. You can see how many groups there are at the right of the scroll bar. If you click on Mark Bad. Mark Bad/ Mark Group/ Unmark Group Tools.25 0. This is the smallest group. It tries to reshape the triangles with a quality parameter value below the indicated maximal threshold. 2. all poor quality triangles will be marked. turn on grouping and browse to the interesting groups and mark the bad triangles. grouping is a very powerful tool to find bad edges. Tip: Grouping works on all the parameters. 3. Depending on the boundary level. As such. For Mark group.

3. the algorithm tries to make triangles that all have a quality above the maximum threshold value Maximum geometry error: This is the maximum allowable deviation between the part’s surface before and after the automatic remeshing. This operation often file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.5 0. Select the quality parameter you like to measure the quality of the triangles with.Import Page 74 of 169 Equi-angle skewness (Normalized) Stretch 0. Minimal edge length: This parameter sets a limit on the length of the edges of the triangles that will be created during remeshing Number of iteration: The amount of times the program will try to make the triangles of better quality. Max edge length: The maximum edge length will limit the longest edge of the generated triangles.1 Remark: Automatic remesh operations are only possible on the parameters in the dropdown list next ot the Q and G letter. we recommend using values in between 2 and 5. the post-processing will be activated. Parameters Maximum quality threshold: You can define a maximum quality threshold value here. 2. If you fill in 0. Number of move iterations: This is a post-processing step in addition to the split-based algorithm. the post-processing step is deactivated. Typically. It may be that high quality triangles can be made. Preserve initial mesh quality: The refiner algorithm starts with a reduce triangle operation. which further optimizes the mesh quality. Automatic remeshing: Split-Based Menubar: Tools:/Auto Remesh/ Split Based method Icon: The program will ask you to determine some parameters before remeshing the part. Choose the remesh algorithm and fill in the parameters. Here you determine how much attention the algorithm should spend on the two of them relatively. or in the part quality sheet by filling in the field or sliding the green bar. Determine the Maximal threshold. at the expense of the geometry. So before you do an automatic remeshing: 1. Higher values tend to make the calculations longer and lower values have little effect. The I parameters are used for mesh inspection purposes. Remark: In the settings (Menubar/ Settings/ Preferences/ General/ Remeshing) you can define the following parameter: Geometry-quality weight ratio: During remeshing a geometric error may be introduced (the difference between the surface before and after the remeshing).htm 2/3/2014 . If you fill in a value bigger than zero. During the remeshing.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Local: It is possible to mesh in local areas. as they look further for neighbors compared to the 1-ring algorithms. the remesh algorithm is applied to the marked triangles Automatic remeshing: Growth factor Once the split based remesh is done. When you start the remesh operation on a file that already has a fairly well mesh. the remesh based on growth factor can be used. During the remeshing. This has the effect that the growth is smoother over a longer distance. The best results can be expected from the 2-. Local: It is possible to mesh in local areas. Minimal edge length: This parameter sets a limit on the length of the edges of the triangles that will be created during remeshing Max edge length: The maximum edge length will limit the longest edge of the generated triangles. This can cause problems when generating a 3D mesh from the surface mesh. When checked. or 3-ring algorithms. the algorithm tries to make triangles that all have a quality above the maximum threshold value Growth threshold: This threshold value determines which triangles need to be improved and until where the algorithm will control the growth. To smooth the transitions from small to large triangles. it can happen that the growth of the triangles is too big. or in the part quality sheet by filling in the field or sliding the green bar. When checked. The program will ask you to determine some parameters before remeshing the part Maximum quality threshold: You can define a maximum quality threshold value here. the remesh algorithm is applied to the marked triangles The effect of the growth algorithm is shown in the figures below.Import Page 75 of 169 introduces long thing triangles and in general triangles that are far from equilateral. Number of iterations: The amount of times the program will try to make the triangles of better quality.htm 2/3/2014 . it is advised to skip the reduce step of this algorithm. Maximum geometry error: This is the maximum allowable deviation between the part’s surface before and after the automatic remeshing.

Based method The program will ask you to determine some parameters before remeshing the part. During the remeshing. the algorithm tries to make triangles that all have a quality above the maximum threshold value. Remark: In the settings (Menubar/Settings/Preferences) you can define the following parameter: Geometry- file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 .Import Page 76 of 169 Automatic remeshing: Optimize-Based Menubar: Tools:/Auto Remesh/ Optimise. Maximum geometrical error: This is the maximum allowable deviation between the part’s surface before and after the automatic remeshing. Parameters Maximum quality threshold: You can define a maximum quality threshold value here. or in the part quality sheet by filling in the field or sliding the green bar.

the algorithm will not take into account the bad edges. Number of iterations: This defines how many times the program should make the calculations. Use post processing: After the optimization scheme. It may be that high quality triangles can be made. Parameters Tolerance: If 2 triangles are replaced by one triangle. Local: When Local is set. The reduce mode The Point-type reduction: This mode will try to reduce the amount of triangles by removing a point. at the expense of the geometry. Skip bad edges: When you mark this box. This results in less low quality triangles especially for moderate to medium maximum quality thresholds. Max edge length: The maximum edge length will limit the longest edge of the generated triangles. the edge between file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Triangle reduction Normal Triangle reduction Menubar: Tools/Automatic Remeshing/ Triangle reduction/Normal Icon: Description: You can reduce the number of triangles in an STL file. The angle: The Angle-value defines two limits: 1.htm 2/3/2014 . This will speed up the process. Doing a triangle reduction twice with the same Number of Iterations value gives the same result as doing it once with the Number of Iterations value doubled. You can reduce the triangles of the whole part. they may not be reduced. When two triangles have an angle value bigger than Angle. the more triangles will be considered. the algorithm will attempt to improve the remaining low quality triangles using a post-processing subdivision scheme.Import Page 77 of 169 quality weight ratio: During remeshing a geometric error may be introduced (the difference between the surface before and after the remeshing). The closer the value is to 1. or only a selected portion. The tolerance indicates the maximum deviation allowed between the original surface and the new one. The Edge-type: This mode will remove a triangles edge (two points + the connecting line between these two points). Some neighboring triangles can be changed. only the marked triangles will be reduced. Subdivision strength: This parameter limits the quantity of triangles that will be subdivided during remeshing. it may be that there is a little deviation in position. Number of optimizations: The number of iterations after each subdivision during which produced triangles will be optimized. Here you determine how much attention the algorithm should spend on the two of them relatively.

no edge will be added. In this case it is better to perform a smoothing first. When there is no critical edge. This will speed up the process. essential part information may get lost.Import Page 78 of 169 them may not be eliminated. Max edge length: The maximum edge length will limit the longest edge of the generated triangles. Remark: Because of the previous remark it is advisable not to use the reducer on very noisy objects. Where there is no edge. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Maximum geometric error: This is the same as Tolerance: If 2 triangles are replaced by one triangle. The tolerance indicates the maximum deviation allowed between the original surface and the new one. Otherwise too much geometrical information would be lost. the reduction will keep the edge but reduce the number of points on the edge. Doing a triangle reduction twice with the same Number of Iterations value gives the same result as doing it once with the Number of Iterations value doubled. Filter Sharp triangles Icon: When the part has long thin triangles. Quality threshold: This value indicates the level below which no new triangles will be created. 2. Remark: If the tolerance and angle values are too big. This means: where there is an edge there will remain one. it may be that there is a little deviation in position. but will not create triangles that will have a value of the selected quality measurement below the indicated maximum threshold. Quality Preserving triangle reduction Menubar: Tools/Automatic Remeshing/ Triangle reduction/Quality Preserving Icon: Description: This reducing algorithm will reduce the amount of triangles. Skip Bad edges: The remesher will not take into account the bad edges. When the program meets such an edge.htm 2/3/2014 . Number of iterations: This defines how many times the program should make the calculations. this Angle-value determines the maximum angle that can be created during the reduction. this filter will remove the sharp triangles.

Detect self-intersections When pressing the button . The surrounding triangles are not modified. depending on your choice.Import Page 79 of 169 Filter: Triangles thinner as this distance will be marked or deleted. which re-arranges slightly the surrounding triangles to close the gaps. The intersecting triangles will be marked and can then be removed manually. Smoothing Menu: Tools – Smoothing Description: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. These areas are not real intersections and are not detected with this function. This is easy to filter only thin triangles of folds and leave thin triangles of curves untouched. To detect sharp areas in a part.htm 2/3/2014 . the model will be checked for self-intersecting triangles. use the sharp geometry inspection measure. Mark: The selected triangles are only marked. Collapse: The selected triangles will be collapsed. Angle: The thin triangle will only be selected when the angle it makes with its neighbors is bigger as the given angle. Delete triangles: The selected triangles are deleted. Note: Sometimes sharp edges can also cause problems when generating a 3D mesh.

Iterations: The remesher will perform the smoothing multiple times Advanced Options Avoid inverted triangles: To avoid the creation of flipped triangles. Shrinkage compensation factor: The smoothing algorithm has the side effect that the part is shrinking. The new position is still 50% dependent on the old position. the dependency is spread over the points. the movement of the points will be aborted when the angle between the normals of the neighboring triangles is bigger as the given angle.this means that point is actually moved in opposite direction (out of "smooth" position). so points "oscillate " forwards and backwards.01) the new position is mainly dependent on the old position of the point. Local will smooth only the selected triangles. the point won't be moved. Smooth Factor: We will explain this factor with the figure below. In this last case it is obvious that we talk about smoothing. Use Curvature Smoothing: Curvature smoothing tries to choose the new position for points based solely on geometry Remark: Be careful. The algorithm changes the position of this center point according to the positions of the eight other points. The importance of the other points can be raised or lowered by adjusting the Ratio-parameter. When using too high values for these parameters. With high values for the ratio. Manual Remeshing file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The figure shows eight triangles with one common point in the center. This factor will compensate this. This compensation step is similar to the first one except that the parameter has a negative sign .htm 2/3/2014 . the shape of your part could disappear.Import Page 80 of 169 General Options Global/Local: Global will smooth the whole part. If this ratio is 1. This algorithm is exercised on every point of the part. the new position is mainly determined by the position of the other points of the triangles. If this Ratio is low (0. Skip Bad Edges: When the point is at a bad edge.

you can enter a threshold value. the delta value will have a negative sign. The delta value expresses the difference (after-before). and a warning will be given. The delta value expresses the difference (afterbefore). a number of triangles will be selected that will undergo the remeshing operation.htm 2/3/2014 . Before you do the operation. Affected Triangle List When you want to perform a manual operation. Quality after: Depending on the manual operation. The process can be followed with the triangles quality toolsheet. A geometric error above this threshold will be displayed in red and so attract your attention. a number of triangles will be selected that will undergo the remeshing operation. the remesher will always show you when you point your mouse to file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Depending on the operation. the remesher will show you the error that will be introduced. one. Based on this value you can decide whether or not to perform the operation. Triangle Quality Quality before: Depending on the manual operation. The quality thus diminished. Average (before/after/delta): This row shows the average value of the quality measure of the selected triangles (before the operation) and the resulting triangles (after the remeshing operation is performed). If the qualities measure value of a triangle after the remeshing operation is less than before. Delta: This column shows the difference of the values displayed in the quality after and the quality before columns.Import Page 81 of 169 You can remesh manually which allows you to perform a number of local remesh operations on a selected number of triangles of the part. This column shows you the value of the selected quality measure of these selected triangles before the operation is performed. In the Settings (see Menubar/Settings/Preferences/ General/ Remeshing). Minimum (before/after/delta): The lowest quality measure value of all the selected triangles (before the operation) and resulting triangles (after the operation) is shown. two or more triangles are involved. The triangles quality sheet Menu: View/ Triangles Quality sheet Icon: Geometrical error Due to the remeshing operation a geometrical error may be introduced. This column shows you the value of the selected quality measure of these selected triangles before the operation is performed.

Flip edge . The corner points of the triangles. Collapse edge When a triangle has one very short edge and a long height it is a very long thin triangle (we call it a needle). the operation will be done. and the value of the triangles that will be formed when the operation should be done. When you point to a short edge. the operation is canceled. If you release the ctrl button first. The toolbar is positioned at the left of the screen at start up. the edge will collapse. When you point your mouse to an edge. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. Collapse triangle file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The point where the edge end points collapse is shown in red.Import Page 82 of 169 the triangle or edge you want to adapt. the edge will be flipped. will move to the new point. which have the short edge as border will disappear because the remesher brings the two end points of the edge together in a new point which is positioned on the edge.htm 2/3/2014 . When you click. and will outline in green the edges of the triangles that will result. the triangles that will be involved in the operation. When you click. you will not see all the values of the quality measurements in the list. These kinds of triangles can be removed with the collapse edge tool. If you then release the mouse button. that had these end points as corner. The triangles. the remesher will color the two adjacent triangles and show the flipped edge in green. and you can move the mouse pointer to the scroll bar of the list and scroll. When there are many triangles involved. The manual remeshing tools Menu: Tools/Manual remeshing Menu: View/Remesh Toolbar/Icons or Measure single triangle quality If you click on this icon and point to a triangle the value of the selected quality measure will be shown in the Triangle Quality Sheet. In the Triangles quality sheet you can see the value of the selected quality parameter of the present triangles that will be involved in the operation. and the edges of the ones that will be there after the operation in green. Press and hold down the control button. The edges of the triangles that will be there after the operation are shown in green. because it is too short and you need to scroll. the remesher shows the present triangles in a white dotted line and colors them.

The other corner point of the edge will be projected perpendicular on the edge opposite of the cap corner point. The edges of the triangles adjacent to the triangle that is removed. and the edges of the triangles that are influenced under the operation in green. The corner points of the triangle will be collapsed to a point inside the triangle. the operation is canceled. These triangles can be removed with the collapse cap tool. the triangle will collapse. Cap collapse Triangles that have a very long base and small height (we call it a cap) are far from being equilateral. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. and all have the new point as an end point. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. Cap split (propagating) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. If you release the ctrl button first. If you then release the mouse button. If you release the ctrl button first. If you then release the mouse button. the operation will be done. the operation is canceled. When you click.htm 2/3/2014 . the remesher will show the new corner point in red. When you click. and that had the corner points of the removed triangle as one of the end points. The remesher will show the new point in red.Import Page 83 of 169 Very small triangles can be removed with the collapse triangle tool. will be moved a bit. When you point the mouse to a cap. the operation will be done. This point will be a new corner point. In the cap corner point (see figure above) ends an edge of a triangle adjacent to the cap. If you point to a triangle. the cap will be collapsed. and the edges of the triangles that result after the operation in green.

edges of the selected triangle. When the new created triangle is also a cap (decided if the angle of the cap corner point is very big). a cap is converted into two needles. the edges of the triangles that will be formed after the operation are shown in green. The triangle that has this edge as border. the operation will proceed. The remesher will create two or three new corner points on two or three – respectively. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. the remesher will split it in two. When you point your mouse to a cap. and thus so subdivide a triangle in 3 triangles.Import Page 84 of 169 Triangles that have a very long base and small height (we call it a cap) are far from being equilateral. The new edge will end on the edge opposite the cap corner point (see figure). Subdivide one triangle It is possible to subdivide one triangle in more triangles. This operation introduces no geometrical error. the triangle will be subdivided. This operation introduces no geometrical error. This way. will also be split. These triangles can be split in two with the cap split propagating tool. The remesher will color all the triangles involved and will show the edges of the triangles that will be formed after the operation in green. When you click. When you point the mouse to a cap. Add new point in triangle You can add a point.htm 2/3/2014 . the cap(s) will be split. When you click.

When you click the mouse button. It is possible to move the red point by keeping the control button pushed together with the left mouse button. When you point to a point. Move point You can point the mouse to a corner point and drag the point to a new place. the operation will be done. When you click. the operation is canceled. If you then release the mouse button. and the new corner point in red. The remesher will draw a line between those two points. This operation introduces no geometrical error. the operation will be done. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. Material Assignment file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. and divide all the triangles this lines runs through. If you then release the mouse button. so that the line can be formed by edges of newly created triangles. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button.Import Page 85 of 169 When you point the mouse to a triangle. The triangles adjacent to that will both be divided in two. If you release the ctrl button first. This operation does not introduce a geometrical error. When you point the mouse to an edge the remesher shows the new edges in green lines. The cross point of these edges is shown in red. This operation does not introduce a geometrical error. The adjacent triangles will deform. If you release the ctrl button first. If you then release the mouse button. the operation is canceled. the operation will be done. Create straight edge You can click on two corner points of two different triangles one after another. the program will show it in red. the triangle will be subdivided. the operation will be done. the remesher will show the edges of the triangles that will be formed after the operation in green. the operation is canceled.htm 2/3/2014 . If you release the ctrl button first. The remesher will then create a new corner point on that edge. Add point on edge You can select an edge.

each element has its own gray value based on the image data set. Mimics will show for each grayvalue the amount of elements that were assigned that particular value. A first step that is taken for both methods is discretization: the range of all gray values is subdivided into intervals. This gray value will then be used in further calculations. How this discretization is done depends on the chosen method. Material assignment method Uniform method In the uniform method. For each material the properties can then be defined in the material editor. During the calculation of the grayvalue of each element. Mimics uses an accurate method to assign gray values to elements by calculating exact intersections between voxels. After the grey value calculation. The center file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. no matter how many different material assignments are exported. The gray value assignment is stored in the Mimics project file.Import Page 86 of 169 You can assign materials to FEA meshes via the FEA menu or the FEA mesh tab. Each element is assigned to one mask based on this volume of intersection. the material assignment window will appear: In the Elements Histogram. Before you can assign materials to the elements of the volumetric mesh. The third option to create materials is the Mask method. While being accurate. the discretization of the gray values is done by dividing the range of gray values that occur in the volume mesh into a specified number of equal sized intervals that each represent a material. also the volume of intersection with the different masks in the project is calculated. so the gray value calculation only needs to take place once for each volume mesh in a Mimics project. Two methods can be used to convert this gray value into material properties: Uniform Method and Look-up File Method. Mimics will first calculate a gray value for each element.htm 2/3/2014 . care has been taken that the calculations can be performed efficiently. After the calculation of the gray values of the elements of the volumetric mesh.

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gray value of each interval is chosen as a representative for that interval. After you have entered the amount of materials in the edit box, you can preview the material assignment by clicking on the Preview button. The color of the elements will be determined according to following color scale:

Look-up File Method
For this method a look-up file is specified that indicates which intervals are used to divide the range of gray values (look-up files can also be expressed in Hounsfield units). Each interval can be assigned a specific density value. A lookup file can be chosen by clicking on the Load button. It is possible to call the default viewer or editor for the specified look-up file by clicking on the Open with button. After you selected the correct look-up file, you can preview the material assignment by clicking on the Preview button. The color of the elements will be determined according to following color scale:

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The format of the lookup table is very simple. The first line specifies the xml format of the file. In the header of the xml file, the version of the file can be specified (1.0 for the moment). Ranges of grayvalues are specified by their first boundary in the Start tag. The Density tag specifies the density that should be associated with the material. Example: <?xml version="1.0" encoding="UTF-8"?> <LookupTable> <Header> <Version> <Major>1</Major> <Minor>0</Minor> </Version> <Units>Hounsfield</Units> </Header> <Table> <Interval><Start> 0.0e0 </Start><Density> 0.0e0 </Density></Interval> <Interval><Start> 3.0e2 </Start><Density> 3.0e2 </Density></Interval> <Interval><Start> 6.0e2 </Start><Density> 6.0e2 </Density></Interval> </Table> </LookupTable> This Lookup file specifies 3 materials: 1. 2. 3. Material 1 contains all elements with HU (Hounsfield Unit) between 0 and 300. That material is assigned a density of 0 Material 2 contains all elements with HU between 300 and 600. That material is assigned a density of 300 Material 3 contains all elements with HU between 600 and 3071. (HU is maximal 3071). That material is assigned a density of 600

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Note: You can choose between "Hounsfield" or "Grayvalue" as the Unit type.

Mask Method
By using the material assignment from mask, you can use the segmentation in your project to assign materials to your elements. For each used mask, one material will be created. For each element one of the materials is assigned based on the volume of intersection of that element with each mask. If there are elements in the volume mesh that fall completely outside the selected masks, one extra material is created for those elements. If an element has the same intersection volume with several masks, the first mask in the list is used for assigning a material to that element. When choosing the mask method, click on the Select button to select which masks you want to use:

After this you can see the assignment of the materials in the histogram:

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Note: if you change one of the masks after doing the grayvalue calculation and choose to do a material assignment from masks, Mimics will have to calculate the grayvalues again.

Material Expressions
Density Expression
The density expression can be used for translating the grayvalue of an element to a density when using the uniform method. To do this, an empirical expression of the form A+B*X^C+D*X^E can be entered to convert the gray value into a density value. This method can also be used to export gray values: if 0+1*X^1 + 0*X^1 is used as a density expression, the representatives of each interval are written out as densities. Note: For the look-up method, the density for each material is taken from the look-up file. For the mask method you have to enter the density for each material yourself in the material editor.

E-Modulus expression
Based on the density value, an expression can be entered to define the e-modulus for each material. The entered expression will only be used if the checkmark is enabled. If there is no density value available for a certain element, the e-modulus value will also remain empty.

Poisson expression
Based on the density value, an expression can be entered to define the poisson coefficient for each material. The entered expression will only be used if the checkmark is enabled. If there is no density value available for a

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certain element, the poisson coefficient value will also remain empty.

Material Editor
The assigned materials and their properties can be displayed and adjusted in the material editor. You can change the value of one of the fields by right-clicking twice on the value. You can also adjust multiple values at the same time by selecting them and filling in a new value. Fields that are empty in the material editor will either not be exported or will receive a value of 0 depending on the export format.

The color of each material can be changed by double-clicking on the color box:

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Note: about units (Hounsfield units/Gray values): Hounsfield units are the unit image data that comes from medical scanning devices. Gray values is the unit that is used internally in Mimics. Both units relate as value in GV = value in HU + 1024. Mimics has a preference setting to select which unit is used in the user interface (Options -> Preferences -> General -> Pixel Unit). Warning: the current unit is also used for the density expression. Note: most FEA softwares do not allow you to enter a density with a negative value, so make sure you choose your expression accordingly or adjust the values manually in the material editor.

Using Mimics with Patran
Export a surface file to Patran
After you have calculated a surface mesh and remeshed it to make it suitable for FEA purposes, you can export this surface mesh to an Patran neutral file. To do this, go to the Export menu and choose Patran. This will open following interface:

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You can export a 3D Object or an STL file to an Patran neutral file, by adding the object to the list, choosing the Neutral File format and clicking on the OK button.

Convert a surface mesh to a volumetric mesh
This surface mesh can be imported in Patran by going to the File menu and choosing “Import”. This will open following dialog:

Make sure you use the same settings as above. After the import of the mesh, choose the Elements button in the toolbar and choose to create a solid mesh. Choose to create a Tetmesh with Tet4 or Tet10 elements. Have a look at the settings below how to do this:

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choose to select triangles and select all triangles in the mesh.Import Page 94 of 169 Next. You can export this volume mesh by going to the File menu and choosing Export. After clicking on the Apply button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 . a volume mesh will be generated.

Then browse to the directory where the files are located.Import Page 95 of 169 Import the Patran volume mesh You can import a Patran neutral file by clicking on the Import button in the FEA project management tab: This will open a file chooser: Change the type of the listed files to Patran Neutral if needed and all Patran files will be shown. select the correct file and click on the Open button.htm 2/3/2014 . the files will be imported. Supported element types The Mimics FEA module supports four types of Patran elements:   5 (4-node tetrahedron) 7 (6-node wedge) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

Using Mimics with ABAQUS Export an ABAQUS surface mesh You can import an ABAQUS surface mesh by going to the Export menu and choosing the ABAQUS format. Supported Patran packets The Mimics FEA module supports 6 Patran packets:       25 (File title) 26 (Summary data) 1 (Node data) 2 (Element data) 3 (Material properties. the others are set to 0.Import Page 96 of 169   8 (8-node hexahedron) 5 (10-node quadratic tetrahedron) If you require other elements types. Mimics assigns only 7 of them. 27-29 (E-modulus). file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. export only) 4 (Element properties. please let us know and we will try implement those elements in our future releases. In the following interface you can then add 3D Objects or STLs and export them to ABAQUS surface meshes. For E-modulus and Poisson coefficient all three properties contain the same value.htm 2/3/2014 . export only) Material properties: Patran writes out 96 material properties. 30-32 (Poisson coefficient). Exported material properties: 2 (density).

Import Page 97 of 169 Convert the surface mesh to a volume mesh Import the surface mesh In ABAQUS/CAE.htm 2/3/2014 . Depending on the version of ABAQUS you have choose one of the following workflows: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Browse to the directory where you have saved the model and select to import it. go to File->Import->Model.

Then again choose to convert your mesh from tri to tet.. Export a volume mesh After the conversion of the mesh you can export your volume mesh by going to the Job Module and choose to Create a Job.5 In ABAQUS 6.htm 2/3/2014 .5 you should go to the Mesh module.Import Page 98 of 169 Conversion in ABAQUS 6. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.. This will open following dialog: After choosing the Conversion of Tri to tet. click on OK and the surface mesh will be converted to a volume mesh. choose the Mesh menu and the Edit .4: Switch to the Part Module and choose to Edit the Mesh. Conversion in ABAQUS 6. option.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Then you can go to the Job menu and choose the Write Input option to export an . click on Continue.htm 2/3/2014 . This .Import Page 99 of 169 After choosing a name for your Job and choosing the correct model.inp file. After this a Job is created for your model.inp file should be imported again into Mimics. This will open following dialog: Choose to use the default settings and click on OK.

The structure of the file should be: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 100 of 169 Import the ABAQUS volume mesh in Mimics You can import an ABAQUS volume mesh by clicking on the Import button tab: in the FEA project management This will open a file chooser: Change the type of the listed files from Patran Neutral to ABAQUS File and all ABAQUS files will be shown. the files will be imported. select the correct file and click on the Open button. Then browse to the directory where the files are located. The ABAQUS file There are some limitations for the format of the ABAQUS file.htm 2/3/2014 .

432. MATERIAL=<name> The *MATERIAL command: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. There should be an empty line between the *HEADING section and the *NODE command and between the *NODE section and the *ELEMENT command and after the *ELEMENT section. 54.94200134277344 2. The commands *HEADING and *NODE should not have any text or spaces behind them. Supported element types The Mimics FEA module supports four types of ABAQUS elements:     C3D4 (4-node linear tetrahedron) C3D6 (6-node linear triangular prism) C3D8 (8-node linear brick) C3D10 (10-node quadratic tetrahedron) If you require other elements types.htm 2/3/2014 . 14874. -158. 14869. *NODE and *ELEMENT should be written in capitals.1038970947266. 347. ELSET=<name> The *SOLID SECTION command: *SOLID SECTION.51170015335083 … *ELEMENT. 14870. ELSET=<name>. 14869 … Three important rules to follow are:    The commands *HEADING. TYPE=<type>. 14872 474605. -245. type=C3D4 474604. 14868.597900390625. Supported ABAQUS commands The Mimics FEA module supports 5 ABAQUS commands:      *HEADING *NODE *ELEMENT *SOLID SECTION *MATERIAL The *SOLID SECTION and the *MATERIAL command are only used during export and are ignored during import. 14874. please let us know and we will try implement those elements in our future releases.Import Page 101 of 169 *HEADING *NODE 1.5975952148438.3656005859375. The *ELEMENT command: *ELEMENT. 14873. 4. elset=region0.

NAME=<name> *DENSITY <material density> *ELASTIC <E-modulus>. Element-based: The part is exported as a mesh. the FVMESH command should be used. To generate the volume mesh in Ansys. Convert a surface mesh to a volumetric mesh in Ansys This surface mesh can be imported in Ansys by going to the File menu in Ansys and choosing “Read Input From”.htm 2/3/2014 . To export add the object to the list. Importing this file in Ansys will result in a remeshing of the file. and will loose the original triangulation.Import Page 102 of 169 *MATERIAL. choose the appropriate Ansys File format and click on the OK button. you can export this surface mesh to an Ansys file. This will open following interface: Mimics can export your remeshed 3D object to Ansys as an Area-based or an Element-based file Area-based: Each triangle is exported as a separate face into the ansys-file. To do this. go to the Export menu and choose Ansys. having triangles as elements. We advice you to use the Element-based export as this will preserve the obtained quality of the mesh. <Poisson> Using Mimics with Ansys Export a surface file to Ansys After you have calculated a surface mesh and remeshed it to make it suitable for FEA purposes. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

To mesh the areas to elements.1. In the MeshTool check smart size and put it to coarse.g.SHELL93. Or in the main menu select Preprocessor | Element type | Add/Edit/delete and add a surface element type. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. You can do this with the ET command e. go to Main Menu > Preprocessor > Meshing > MeshTool. ET.htm 2/3/2014 . Select as mesh Areas and as Shape Tri and free.Import Page 103 of 169 Convert an Area Based surface mesh to a volumetric mesh First select an element type to which you want to assign the surface mesh.

htm 2/3/2014 .Import Page 104 of 169 Click on Mesh. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. In this dialog click on pick all. the Mesh areas dialog pops up.

Add a solid element type to generate your volumetric mesh. MODMSH. ET.Import Page 105 of 169 To release all associations between the current solid model and finite element model. you can do this with the ET command e.htm 2/3/2014 .detach.2. If you want to load your volume mesh back into Mimics for material assignment you should use one of the following element types: SOLID72 (linear tetrahedron) SOLID92 (quadratic tetrahedron) If you require other elements types.SOLID92. please let us know and we will try to implement those elements in our future releases. Convert an Element Based surface mesh to a volumetric mesh In Ansys select File | Read input from and load the file file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. To generate the volume mesh you should use the command FVMesh or you can execute this command from the main menu Preprocessor | Meshing | Mesh | Tet Mesh From | Area Elements. Or in the main menu select Preprocessor | Element type | Add/Edit/delete and add a solid element type. execute the command.g.

Import Ansys files in Mimics As stated in the Mimics help file.2.htm 2/3/2014 . you can again do this with the ET command e. To generate the volume mesh you should use the command FVMesh or you can execute this command from the main menu Preprocessor | Meshing | Mesh | Tet Mesh From | Area Elements. These three files are the PREP7 file. click on the Import button in the FEA project management tab: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. KOP6. ET.Mesh200) Add a solid element type to generate your volumetric mesh. KOP3. Note: If desired you can change the surface element type with the command ET. ITYPE. INOPR (e.g. To import the PREP7 file. KOP4. KOP2.1. Or in the main menu select Preprocessor | Element type | Add/Edit/delete and add a solid element type. Ename. et. KOP5. If you want to load your volume mesh back into Mimics for material assignment you should use one of the following element types: SOLID72 (linear tetrahedron) SOLID92 (quadratic tetrahedron) If you require other elements types. please let us know and we will try implement those elements in our future releases. a file with a list of the elements and a file with a list of the nodes.g. KOP1. the Mimics Ansys importer needs three different ASCII files as input.SOLID92.Import Page 106 of 169 The surface element type is Shell93 by default. More information about these three files can be found further in this document. Mimics requires the user to import only the PREP7 file: Mimics will use the references to the two other files in the PREP7 file.

The PREP7 file The Ansys PREP7 file contains references to the nodes and elements files and material property definitions.26407.'AnsysTest_nodes_file'. Then browse to the directory where the files are located. the files will be imported.SOLID92 NRRANG. An example of such a file (without material properties) can be found below: /PREP7 ET.1 EREAD.' '.' ' file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.1 NREAD.17317.1.2.'AnsysTest_elements_file'.1.htm 2/3/2014 .' '.' ' ERRANG. select the PREP7 file and click on the Open button.Import Page 107 of 169 This will open a file chooser: Change the type of the listed files from Patran Neutral to Ansys File and all files will be shown (Ansys files do not have a general extension).

KAPPND With parameters:     Fname: File name (32 characters maximum) Ext: File name extension (8 characters maximum) Dir: Directory name (64 characters maximum) KAPPND: Append key: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The third parameter ( ) is the directory the file was written out to (we suggest to not use a directory) ERRANG. The third parameter (1) is the increment of the indices of the elements and will be 1 in most cases.2. These parameters can be derived from the Node status. The index of the first node is equal to the maximum node number minus the number of nodes defined plus 1. Dir. The second parameter (26407) should be equal to the maximum node number. The second parameter ( ) is the extension of the file (we suggest not to use an extension).26407. The third parameter ( ) is the directory the file was written out to (we suggest to not use a directory) The nodes file The nodes file contains the coordinates for all nodes.htm 2/3/2014 . Ext. You can also write out the nodes file with following command: NWRITE.number of elements defined + 1) EREAD. 17317.1.1 The first parameter (1) is the index of the first node and will be 1 in most cases.1. The element status dialog is evoked by executing the following commands: ELEM STAT The element status lists the maximum element number and the number of elements defined. (index of first node =maximum node number .' '. The third parameter (1) is the increment of the indices of the nodes and will be 1 in most cases.SOLID92 The first parameter (2) is the local element type and depends on your Ansys project.'AnsysTest_elements_file'. /PREP7 This command indicates to Mimics that the file is a PREP7 file ET.' '. The index of the first node is equal to the maximum element number minus the number of elements defined plus 1.'AnsysTest_nodes_file'.' ' The first parameter (AnsysTest_elements_file) is the filename of the elements file. (index of first element =maximum element number .Import Page 108 of 169 This PREP7 file should be created manually. The easiest way is to copy the text to a new file and adapt it to your needs. Fname.1 The first parameter (1) is the index of the first node and will be 1 in most cases. These parameters can be derived from the element status.' ' The first parameter (AnsysTest_nodes_file) is the filename of the nodes file. The file can be written out in Ansys by going to: Main Menu > Preprocessor > Modeling > Create > Nodes > Write Node File. The second parameter ( ) is the extension of the file (we suggest not to use an extension). The second parameter (17317) should be equal to the maximum element number. The node status dialog is evoked by executing the following commands: NODES STAT The nodes status lists the maximum node number and the number of nodes defined. The second parameter (SOLID92) is the type of the elements that is used in the mesh NRRANG.number of nodes defined + 1) NREAD.

htm 2/3/2014 . Dir. Note: We suggest to write out the elements file in the LONG format.Import Page 109 of 169 o o 0 . Supported element types The Mimics FEA module supports two types of elements:   SOLID72 (linear tetrahedron) SOLID92 (quadratic tetrahedron) If you require other elements types.Append data to the end of the existing file Note: We suggest to write out the nodes file without an extension. It’s strongly advised to write out the elements file in the LONG format.Append data to the end of the existing file Format: Format key: o o SHORT .I6 format (the default) LONG1 . you have to write out in the LONG format or Mimics will refuse to import the files.Rewind file before the write operation 1 . The file should be written out with following command: EWRITE. Ext. If you have more than 99. KAPPND. Fname. The elements file The elements file contains the definitions for all elements. Format With parameters:     Fname: File name (32 characters maximum) Ext: File name extension (8 characters maximum) Dir: Directory name (64 characters maximum) KAPPND: Append key: o o  0 .I8 format Note: We suggest to write out the elements file without an extension.Rewind file before the write operation 1 . Supported material properties The Mimics FEA module supports three types of material properties:    DENS (Density) EX (E-Modulus) PRXY (Poisson coefficient) Supported PREP7 commands file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.999 nodes. please let us know and we will try implement those elements in our future releases.

<material property>.<max>.<drive+directory> The MP command: MP. You can export your 3D object to an Abaqus file by going to the Export menu and choosing Abaqus.Import Page 110 of 169 The Mimics FEA module supports 6 PREP7 commands:       ET MP NRRANG NREAD ERRANG EREAD The ET command: ET.<type> The NRRANG/ERRANG commands: NRRANG.<local type element number>. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.<filename>. clicking on the Add button and then clicking on the OK button.<value> Using Mimics with Simmetrix Export surface meshes from Mimics We advice to use the Abaqus file format when linking between Mimics and Simmetrix.<file extension>.<min>.<material reference number>.htm 2/3/2014 .<increment> The NREAD/EREAD commands: NREAD. This will show following dialog: You can export a 3D object from the list by selecting it.

$z" } # Set element-code based on mesh degree map = "<1 'C3D4'> <2 'C3D10'>" element-code = function:mapI2S($meshDegree. first go to the export/case/abaqus folder in the root directory of the SimAppS folder and make a backup of the abaqus. $y. $x."C3D???") # Write element sets. After this open the abaqus. To do this.g. only support linear tetrahedra file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.sxp file in this folder.sxp created 28-Jan-2004 jat # Write abaqus input file from input mesh # Use mesh node ids required = "mesh" precision showpoint = 16 =1 # (runs faster when "off") mfaceNormals = "off" mregionIdOffset = 1 # Create mesh nodes mesh { nodeMessage = function:makeNodes() log:header = "$nodeMessage" } # Write first header header = "*HEADING\n" # Write mesh nodes mesh/mnodes { header = "*NODE\n" item = "$id.$map.sxp file in a text editor (e.Import Page 111 of 169 Change the Abaqus pattern in Simmetrix To make sure that you write out an Abaqus file in Simmetrix that can be imported in Mimics you will have to change the default Abaqus pattern file in the Simmetrix software. 1 for each model region # For now.htm 2/3/2014 . This pattern file will determine how an Abaqus file is written out exactly. notepad) and change the contents of the file to: sxp 0 # abaqus.

Import Page 112 of 169 gmodel/gregions/* { header = "*ELEMENT. Using Mimics and Fluent file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. elset=region$tag. select it and click on the Open button. $(mnodes[*]/id)" } # end context (mregions/*) } # end context (gmodel/gregions/*) # Remove mesh nodes mesh { nodeMessage = function:removeNodes() log:header = "$nodeMessage" } Import Simmetrix files in Mimics Now you can start Simmetrix. You can then start assigning materials to the volumetric mesh.htm 2/3/2014 . type=$element-code\n" mregions { item = "$id. This will open following dialog: Browse to the directory where you have saved the Abaqus volumetric mesh. import the Abaqus surface mesh from Mimics and make a volumetric mesh in Simmetrix. If you export this volumetric mesh to an Abaqus file you will be able to import this file in Mimics to assign materials to it by going to the FEA menu and choosing Import.

Typically. we would end up with many noise surfaces and unclosed wireframe and Gambit will not be able to recognize a volume inside the surfaces. Especially for fluid flow simulation applications. a fluent project contains inlet. you can choose the wireframe that will be used for splitting up the surfaces in this file: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. In the fluent mesh file. which will close the inlet and outlet surfaces. outlet and boundary surfaces. So. we don’t have surface definitions. you need to inspect the noise wireframe. you need to smooth the area to make sure the wireframe is either open or disappears. All triangles within a closed wireframe contour will belong to a separate surface. we need to identify the wireframe angle. surfaces are necessary to define inlet and outlet of the flow. In Mimics. We use the wireframe in to do this. As long as the noise wireframe is not closed. As the wireframe of STLs can be noisy. If it is not possible to find the wireframe angle which still closes inlet and outlet surfaces and removes all noise wireframe. there is no problem. This is where the Fluent mesh file proves its usefulness. Note that increasing the wireframe angle will open the inlet and outlet contours at some point. This will open following dialog: When you click on OK.htm 2/3/2014 . it is best to use the fluent mesh format. we can write correct surface definitions to make sure Gambit will recognize the volume. Export the object to a Fluent file When you have determined a good wireframe angle. especially for scanned parts.Import Page 113 of 169 To facilitate data exchange with Fluent. so we need a way to define surfaces on the STL. you can go back to Mimics and export the file by going to the Export menu and choose Fluent. we can modify the wireframe angle in the view toolsheet to a value. If there is some noisy wireframe on the boundary surface. The msh file contains the triangle data from the STL file along with surface definitions. which fits our needs. If only an STL is available. In the remesher. we need to make sure this wireframe disappears by choosing a higher wireframe value or by altering the surface of the mesh. Gambit (Fluent’s preprocessor) will read in the STL and split the STL in surfaces according to a feature angle (comparable to our wireframe angle). If it is closed. The notion of surface definitions is important and therefore the msh file contains more information than the STL file.

506 E = 0. strength.and stiffness.93 0.01 *  ^ 1.205 * HU + 139  = 1.91 0.30 R² 0.205 * HU + 139  R² 0.86 E = 3.90 0.205 * HU + 139  = 1.95 0.htm 2/3/2014 .Import Page 114 of 169 Import the surface mesh in Fluent You can then import this fluent file in fluent by using following parameters: Empirical Expressions The tables below show some relationships between different density-.84 0.82 *  ^ 1.85 0.82 E = 2.067 * HU + 131  = 1.423 E = 0.89 0.205 * HU + 139  = 1.99 *  .94 Sca Ref Tec S1 S1 S1 S1 S1 R1 R1 R1 R1 R1 T1 T1 T1 T1 T1 file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.48 R² 0.27 *  .384 E = 0.416 E = 0.31 .91* .84 Axis A-P A-P M-L M-L S-I Young's modulus E (MPa) E = 0.004 * ^ 2.657 E = 0.27 E = 5.77 Axis A-P A-P M-L M-L S-I S-I S-I Young's modulus E (MPa) E = 0.Distal Apparent density   = 1.77 0.77 0.79 E = 2.067 * HU + 131  = 1.84 0.77 0.89 0.77 0.205 * HU + 139  = 1.84 0.01 E = 3.205 * HU + 139  = 1.Proximal Apparent density   = 1. Expressions for Trabecular/Cancellous Bone Expressions for the Femur .91 0.067 * HU + 131 R² 0.91 0.84 *  .84 0.067 * HU + 131  = 1.58 *  ^ 1.01 *  ^ 1.01 *  ^ 1.067 * HU + 131  = 1.77 0.related parameters.64 *  .65 *  ^ 1.92 Sca Ref Tec S1 S1 S1 S1 S1 S1 S2 R1 R1 R1 R1 R1 R1 R2 T1 T1 T1 T1 T1 T1 Expressions for the Femur .84 0.

1327 E = 3.86 0.86 0.89 0.06 *  ^ 1.82 *  .97.91 0.11 *  ^ 0.82 R² Axis A A-P M-L S-I Young's modulus E (MPa) E = 1.1352 E = 0.92 0.85 0.35 E = 8.83 0.80 Axis A-P Young's modulus E (MPa) E = 0.56 *  .95 .916 * HU + 114 R² 0.69 0.0586 *  + 178.349 E = 0.Import Page 115 of 169  = 1.976 E = 0.122 * HU + 47  = 1.88 0.99 -1002 R² 0.20 *  .89 Sca Ref Tec S1 R1 T1 file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.87 0.86 0.331 E = 1.22 .86 0.55 E = 0.122 * HU + 47  = 1.68 E = 5.0005 *  ^ 2.83 0.49 *  .122 * HU + 47  = 1.37 *  .24 *  ^ 0.57 E = 2.75 E = 0.83 0.02 *  ^ 1.79 0.96 Sca Ref Tec S1 S1 S1 S1 S7 S1 S1 S2 R1 R1 R1 R1 R7 R1 R1 R2 T1 T1 T1 T1 T1 T1 T1 Expressions for the Tibia .0041 * ² + 2.22 *  .1142 *  + 54.25 *  .41 E = 4.624 * HU + 173  = 0.Proximal Apparent density   = 0.84 S-I S-I P E = 4.4 E = 0.64 *  ^ 0.001141 * HU + 0.83 0.624 * HU + 173  = 0.88 0.301 R² 0.92 0.06 *  ^ 1.822 E = 1.83 0.122 * HU + 47  = 1.96 0.68 0.69 0.58 Sca Ref Tec S6 S6 S6 S6 S6 R6 R6 R6 R6 R6 T4 T4 T4 T4 T4 Expressions for the Patella Apparent density  Could not be measured Could not be measured Could not be measured Could not be measured Could not be measured Could not be measured  R² Axis A-P A-P M-L M-L S-I S-I S-I Young's modulus E (MPa) E = 0.624 * HU + 173  = 0.209 E = 0.73 0.11837 0.136 *  .57 0.92 0.94 0.91 E = 3.005 * ^ 1.63 *  ^ 1.07 *  ^ 1.60.86 0.69 0.21 E = 3.38.75 E = 7.0019 * HU + 0.97 .92 Sca Ref Tec S1 S1 S1 S1 S1 S1 S2 R1 R1 R1 R1 R1 R1 R2 T1 T1 T1 T1 T1 T1 Expressions for the Major Metaphyseal Regions Apparent density   = 1 * HU  = 1 * HU  = 1 * HU  = 1 * HU  = 0.92 *  .3988 *  + 39.3 E = 5.067 * HU + 131    = 0.448 E = 1.170 E = 0.60 P P Expressions for the Humerus .3665 *  .69 E = 2.90 0.43 0.0057 * ² + 3.6201 *  .94 0.83 Axis A-P A-P M-L M-L S-I S-I S-I Young's modulus E (MPa) E = 2.Lumbar Apparent density   = 1.95 0.644 E = 1.69 R² 0.310 *  ^ 1.88 Sca Ref Tec S1 S1 S1 S1 S1 S1 S2 R1 R1 R1 R1 R1 R1 R2 T1 T1 T1 T1 T1 T1 Expressions for the Spine .122 * HU + 47  0.56 E = 1.04 *  ^ 1.91 0.02 *  ^ 1.172.32 *  ^ 1.htm 2/3/2014 .69 0.51 R² 0.270 E = 5.50 *  .86 0.122 * HU + 47  = 1 * HU  = 1.47 S1 S2 S3 S4 S5 S5 R1 R2 R3 R4 R5 R5 T1 T2 T3 T3 0.105  = 1 * HU  = 1 * HU 0.0976 *  .65 *  .069 R² 0.624 * HU + 173  R² 0.489 R² 0.42 0.169 E = 0.624 * HU + 173  = 0.02 *  ^ 1.Proximal Apparent density   = 0.69 Axis A-P A-P M-L M-L S-I S-I S-I S-I Young's modulus E (MPa) E = 1.624 * HU + 173  = 0.201 E = 0.

4 E = 2132 *  ^ 1.57 0.54 Sca Ref Tec S14 R1 S14 R1 T8 T8 Expressions for the Tibia Apparent density   = 1 * HU  = 1 * HU R² Axis S-I B B Young's modulus E (MPa) E = 0.64 0.80 S-I S-I S-I S-I S-I Expressions for Cortical Bone Expressions for the Mandible Apparent density  R² Axis S-I R Young's modulus E (MPa) E = 0.38 E = 2.55 E = 1.99.61 0.38 E = 1.48134 * r ^ 11.30 Sca Ref Tec S14 R1 T8 S15 R11 T9 S15 R11 T9 Expressions for the Humerus Apparent density  R² Axis S-I C Young's modulus E (MPa) E = 0.00106 * HU + 0.55 0.00106 * HU + 0.4 E = 35.326 E = 0.61 0.8.61 0.74 *  + 59.57 0.96 E = 1.37 0.96 0.00120 * HU + 0.61 0.06 *  ^ 1.38 E = 1.88 0.101 = 0.101 = 0.001 HU  = 1 * HU  = 1 * HU = 0.89 0.33 E = 1173 *  .98 E = 0.86 0.326 E = 0.46 E = 1689 *  .88 0.916 * HU + 114  = 0.011 *  .88 0.44.80 0.95 0.00120 * HU + 0.57 0.2 E = 1371 *  ^ 1.3 *  ^ 6.61 0.0949  = 0.38 .00704 *  E = 0.4 E = 2132 *  ^ 1.101  = 1 * HU  = 1 * HU = 0.99.87 0.93 E = 0.916 * HU + 114  = 0.36 E = 2132 *  ^ 1.63 0.88 S-I S-I S-I S-I 0.11 *  + 76.00130 * HU + 0.29 E = 1.00120 * HU + 0.91 *  + 33.72 0.0 E = 1371 *  ^ 1.63 0.99.htm 2/3/2014 .015 *  .33 E = 1173 *  .540 R² 0.103  = 1 * HU  = 1 * HU = 0.74 E = 1.Import Page 116 of 169  = 0.30 0.33 E = 1173 *  .37 E = 0.916 * HU + 114  0.54 *  + 25.05 R² 0.7 E = 80.80 A-P M-L M-L S-I S-I E = 1.013 *  .52 *  .87 S-I S-I S-I S-I R10 T5 R11 T5 R12 T6 R13 T6 R14 T6 R15 T6 R9 T7 0.55 0.57 0.6 *  ^ 7.55 0.90 0.103 = 0.50 *  ^ 1.66 Sca Ref Tec S14 R1 S14 R1 T8 T8 file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.23.54 *  .89 S-I S-I S-I S-I 0.5 E = 117 *  ^ 7.103 = 0.916 * HU + 114  = 1 * HU  = 1 * HU = 0.33 E = 1689 *  .94 *  + 75.00120 * HU + 0.61 0.63 0.0949 = 0.89 0.013 *  .6 E = 109 *  ^ 6.76 *  + 30.81 *  .44.87 S-I S-I S-I S-I S-I S10 R10 T5 S10 R10 T5 S10 R10 T5 S10 R10 T5 S10 R10 T6 S10 R10 T6 S10 R10 T6 S10 R10 T6 S11 R10 T5 S11 R10 T5 S11 R10 T5 S11 R10 T5 S11 R10 T6 S11 R10 T6 S11 R10 T6 S11 R10 T6 S1 S1 S2 R1 R1 R2 T1 T1 0.0949 = 0.101  = 1 * HU  = 1 * HU = 0.87 0.96 S1 S1 S1 S8 S8 S8 S8 S8 S8 S8 S8 S9 R1 R1 R1 R8 R9 T1 T1 T1 T5 T5 0.024 *  .88 S-I S-I S-I S-I 0.74 R² 0.00130 * HU + 0.46 E = 78.3.55 0.06456 *  ^ 0.61 0.00130 * HU + 0.20 0.80 0.00106 * HU + 0.1 E = 116 *  ^ 6.63 0.53 0.51 *  ^ 1.103  = 1 + 0.63 0.4 E = 1371 *  ^ 1.00130 * HU + 0.85 E = 1689 *  .44.842 E = 0.54 0.55 0.13.80 0.6.46 E = 5.00106 * HU + 0.54 0.0949  = 1 * HU  = 1 * HU = 0.916 * HU + 114  = 0.56 0.124 E = 82.89 0.3 *  ^ 8.

100mA. 4s) / GE 9800 Philips EMI 7070 (140 kVp & 40mA) EMI 7070 (140 kV. Ashman. 1990 Esses. 3s) Literature Reference (Ref) R1 R2 R3 R4 R5 R6 R7 R8 Rho.Import Page 117 of 169 R E = 0. Pongsoipetch. 1989 file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. 3s) EMI 7070 (120 kVp & 50 mA) EMI 7070 (100 kVp & 60 mA) Phillips Tomoscan AV (120 kVp) Siemens Somatom DR3 Phillips Tomoscan AV (120 kVp. Linde.014 *  . 70mA. 1s) Technicare HPS 1440 (130 kVp. 1995 Rho. Hobatho. Brown. Hobatho. 240mAs) GE 8800 (120 kVp) Philips Tomoscan AVE1 (120 kV. Lotz.htm 2/3/2014 .009 *  . Hayes. Zerwekh.69 S14 R1 T8 Expressions for the Femur Apparent density  R² Axis S-I C R Young's modulus E (MPa) E = 0.011 *  . 140 mA. Ashman.007 E = 0.6. Ashman. Goldstein. 150 mAs) GE 9800 CT (120 kVp. Mosekilde.61 Sca Ref Tec S14 R1 S14 R1 S14 R1 T8 T8 T8 Legend Definitions Apparant density = hydrated tissue weight / bulk volume Effective density = (hydrated tissue + marrow weight) / bulk volume Anatomical Axis (Axis) A-P M-L S-I P A R B C Anterior-Posterior Medial-Lateral Superior-Inferior parallel to neck axis Average Radial Bending Circumferential Scanner Types (Sca) S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 Phillips Tomoscan AV (120 kVp. 100 mA.212 0. 1997 Lotz.47 0.6. Kuhn. 150 mAs) Ultrasonic Testing GE 8800 (120 kVp. Cody.087 R² 0.9. 1991 Hvid. Gerhart.4. 1989 Pattijn.010 *  .77 0. 1991 Rho. 2004 Ciarelli. Hayes.142 E = 0. Bentzen.

W... M. 22. Cody. W.. and Hayes.L. Wilson C.B. Linde.A..J.J. 1987 Hvid. Vol. Goldberg. Clift. “Relations of Mechanical Properties to Density and CT Numbers in Human Bone” Medical Engineering and Physics. J.. M.B. Hertig.htm 2/3/2014 . John H. M..P. Goldstein.. Ivan. No. 5 (1995) 347-355 Taylor. Warner. James. and Hollis. R. Rakotomanana. 4.Y. Vol. Lotz.. Edwards. S. Ploeg. Richard B. A.D. R. Bentzen. No. Mosekilde. Lis. H.A... 8/9 (1989) 837-844 McBroom. Steven I.. No. Overview of Simulation Functionality   Anthropometric Analysis Simulation of surgical procedures file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Klabunde. 67-A.R.. Rho. Soren M. Brown. Vol.C. J... Mosekilde. R. Frank. Roland. Ashman. Hayes. M..D. M. 5 (1989) 715-722 Harp.. Jac Y. 8 (1985) 1206-1214 Rho. Jørgensen. Vol. Pongsoipetch... 17. R. 35 (2002) 767-773 Simulation The Mimics Simulation module allows you to simulate surgical procedures. 40 (1997) 157-173 Hvid. Aronson.C. D. 1991 Technique used to determine Young’s modulus (Tec) T1 T2 T3 T4 T5 T6 T7 T8 T9 Ultrasound velocity measurement at 50kHz Destructive compression test (15% strain) Destructive compression test at high strain rate Non-destructive/destructive compression test Destructive compression test Non-destructive compression test Compression test Ultrasound velocity measurement at 2. L. “Prediction of Vertebral Body Compressive Fracture using Quantitative Computed Tomography” Journal of Bone and Joint Surgery. “Determination of Orthotropic Bone Elastic Constants Using FEA and Modal Anslysis” Journal of Biomechanics. “Biomechanical Properties of the Proximal Femur Determined In Vitro by Single-Energy Quantitative Computed Tomography” Journal of Bone and Mineral Research. Linde. No. White. Hobatho. Vol. 301 (1994) 42-48 Hobatho.. Schneider. S.. Buntoing. 5 (1991) 674-682 Esses. Bentzen. No. Vol.T.Import Page 118 of 169 R9 R10 R11 Bentzen.C. 9. Hvid. and Pongsoipetch. 1989 Snyder. E.25 MHz Three point bending References Ciarelli. Vol.. Jeffrey C.E. No. “Evaluation of Orthogonal Mechanical Properties and Density of Human Trabecular Bone From the Major Metaphyseal Regions with Materials Testing and Computed Tomography” Journal of Orthopaedic Research. “X-Ray Quantitative Computed Tomography: The Relations to Physical Properties of Proximal Tibial Trabecular Bone Specimens” Journal of Biomechanics. D. “Noninvasive Determination of Bone Stiffness for Distraction Osteogenesis by Quantitative Computed Tomography Scans” Clinical Orthopaedics and Related Research.. W. Kuhn.. Marcus. Hobatho. Marie-Christine. and Ashman. “Anatomical Variation of Human Cancellous Bone Mechanical Properties In Vitro” Studies in Health Technology and Informatics.

listing the different Simulation functions and Design functions is added. When the module is registered. you probably haven't entered the passwords yet. Note: If you're not able to start the Simulation module. Go to Options > Licenses and fill in the correct passwords. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. You can find this installation file on the Mimics CD or on our website at the Mimics download section. it can be renamed. Starting Simulation All Simulation functions are loaded immediately in Mimics after registration of the Simulation module.htm 2/3/2014 . Extra buttons on the 3D Objects tab: select a 3D Object and click on the Move or Rotate buttons to move or rotate the selected 3D Object. In the Tools menu and in the Tools Toolbar. You can change the visibility by clicking on the glasses. a few extra items are visible in the interface: On the menu bar: An extra CMF/Simulation menu. Simulation tab List of created Objects Name Visible Contour Visible Name of the object. The softtissue simulation module is also listed here in case you also have registered the simulation module. You can change the visibility of the contours by clicking on the glasses. you will have to install the distractor database. there's a Draw/Manipulate Nerve button added. By clicking on the name of the object. Lists if the object is visible or not by means of glasses. Lists if the contour of the objectis visible on the 2D images or not by means of glasses. In the Project Management: Extra Simulation tab.Import Page 119 of 169    Validate design of implants Planning osteotomies and/or distractions Easy repositioning of bone slices both with and without the use of a distractor Note: In order to be able to use distractors in the Simulation Module.

htm 2/3/2014 . You can also define if the cutting path should be closed or not. Deletes the selected objects. depth. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 120 of 169 Diameter Shows the diameter of the Nerve. color. you can change the name. You can choose between Cutting Path. Mirror Plane and nerve. You can also view some information about the distractor. Functions on Objects New Delete Properties This will show the menu of the objects you can create. In the properties dialog of a distractor. thickness and the extensions at the front and the end of a cutting path. The Preview button can be used to preview the adjusted cutting path before applying the changes. you can change the name and color of the distractor. Displays the properties of the selected object: In the properties dialog of a cutting path. Distractor.

width and height of the mirror plane. the Simulation menu appears in the menubar. color and diameter of the nerve. you can change the thickness. you can change the name. Simulation Menu When the Simulation module is licensed.htm 2/3/2014 . In the properties dialog of the nerve. This menu lists different features of the Simulation module: Measure and Analyze file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 121 of 169 In the properties dialog of a mirror plane.

The following window will pop up: Analysis Overview When you click on the 'Overview' button in the Anthropometric Analysis pane. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 122 of 169 To launch the Measure and Analyze tool.htm 2/3/2014 . select the corresponding option from the Simulation menu. the following dialog will emerge.

A window will pop up allowing you to enter the desired analysis name in the ‘Analysis’ field.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.Import Page 123 of 169 Creating a new template To create a new template simply click on ‘New’ in the overview dialog.

htm 2/3/2014 . Each landmark can have some default properties that can be set when creating the landmark or by editing an existing landmark using the ‘Edit’ function. its color and a description. refer to the relevant section in this manual.Import Page 124 of 169 Points When you click on the New button of the Points section. New landmarks can be created. copied. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. a second field in the pop-up window allows you to define landmarks for the analysis. The properties that can be set are the landmark name. The landmark name can only be set at creation time. edited or deleted. If you wish to import existing landmarks.

As for angle. this can be measured using 3 points or using 2 lines (defined by 2 points each). To define a plane you must first have defined points. or -alternatively. For distance either the distance between two points or the distance between a point and a plane can be measured. A convex polygon will be created with those points and the volume will be measured. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. A volume can be measured by selecting at least 4 points. Measurements In the last field. Distances. Note that measurements can only be done using points or planes that have already been defined in the template.Import Page 125 of 169 Planes By clicking on the New button in the Planes section. measurements can be added to the template.you can define a plane based on other planes you have already created in the template.htm 2/3/2014 . angles and volumes can be measured. you can add planes to the template.

A new window will pop up. activate it (the ‘Delete’. Importing Points Adding points from other templates You do not need to define existing points again if you are creating a new template. A green flag will appear. If you wish to edit the properties of one of the default templates you need to first create a copy of the template and then edit the copy.Import Page 126 of 169 Duplicating an existing template If you wish to create a copy of an existing template. should appear behind the template name) and then click on Note: you cannot delete any of the templates that are installed by default with the Simulation module. Simply activate the template in which you wish to import the existing point(s) and click on the button ‘Import Points’. simply click in the ‘Active’ column behind the template you wish to duplicate. Existing points can be imported quite easily from other templates with the ‘Import’ function. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. activate the template by clicking in the ‘Active’ column behind the template. A green flag will appear. Editing an existing template To change the properties of an existing template. Click on ‘Change’ and edit the template as desired. Note: you cannot change the default templates that are installed with the Simulation module. Now click on ‘Copy’ to create the copy. A new window will pop up allowing you to define the template in a similar way as explained under creating a new template.htm 2/3/2014 . Removing an existing template If you wish to remove a template.

Choosing the type of analysis Before starting the analysis you first have to choose the analysis template you wish to use from the Anthropometric analysis pull down menu. since default templates cannot be changed it is not possible either to import points into those templates. go to the Simulation menu and choose Anthropometric Analysis. If points from other templates also need to be imported select that template from the menu and repeat the steps above. select the point(s) you wish to import en click on the ‘import’ button. Of course.htm 2/3/2014 . To finish the import click on ‘ok’.Import Page 127 of 169 From the pull down menu choose the template where you want to import points from. All points in that template are then shown in the window. Getting Started The Anthropometric analysis tool allows for easy analysis and measurement based on pre-defined templates in both 3D and 2D views. To start the Anthropometric Analysis. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

planes and/or measurements as described in the following sections. locate. When you have clicked the Indicate button. first select it from the list and click on the ‘Indicate’ button. the others appear in gray.Import Page 128 of 169 If you do not find a template that coincides with your requirements you can create your own template as described in the creating a new template section. a. Note that you first need to indicate the point before you can use any of the other option in the pane. When you have chosen the template you wish to use. edit or clear the points in the list. Points of analysis The points of the analysis pane provide you with a list of available points in the currently selected template. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Indicating points To place a point. You can indicate a point in both the 2D and the 3D views. indicate the appropriate points. Points that have already been indicated on the images appear in black.htm 2/3/2014 . The pane allows you to indicate. the description of the point will be displayed.

Editing points After having indicated a point you can change its properties. Planes of analysis The pane for the planes of analysis allows you to indicate and edit the planes defined in the template. first enable the right mouse mode by clicking on the Indicate button. Clearing points If you have misplaced a point you can easily remove it by selecting the point in the list and clicking on the ‘clear’ button.htm 2/3/2014 . Locating points If you want to easily view the image on the location where a point was placed. Now you will be able to move the points. If you are not able to select the landmark points. Indicating planes If you select the plane you want to view on the 3D image and click on ‘indicate’ a pop-up will ask you to indicate file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. You can also change the position of the point here by changing its coordinates. This will move both the axial and the sagittal view to the position where the point is located.Import Page 129 of 169 You can always move the points of the analysis after their indication. highlight the point and click on ‘locate’. b. Also a short description of the point you want to locate is given. If you click on the ‘edit’ button you can easily change the color in which the point is shown on the images.

Indicating measurements Select the measurement you wish to indicate and click on the ‘indicate’ button. Viewing/exporting/printing measurement details It is also possible to display a more detailed view of the measurements. values that can be loaded with the ‘Load normal values’ file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. These values can be easily referenced to a set of normal. If these points were already indicated the plane is shown automatically. Click on details and a new window will appear showing all measurements with there pre-operative and post-operative values for both 2D and 3D. Anthropometric 3D measurements If your current template includes measurements. These measurements can be easily indicated on the images.Import Page 130 of 169 the different points that define the plane.htm 2/3/2014 . Editing planes The ‘edit’ option in the planes pane allows you to change the properties of the selected plane. change its color. a list of these measurements is provided in the anthropometric measurements plane. You can choose its thickness. the measurement will have been made automatically. If these points where already indicated on the images. c. width and height and select what opacity the plane should have in the image. A window will pop up to guide you through the placement of the points needed by the measurement.

htm 2/3/2014 . click on ‘Change’ and draw the plane in your axial view. use the ‘Reset’ option.Import Page 131 of 169 option. This overview can be printed out or exported to a csv-file for easy importing in other programs. Sagittal plane In case the CT images were not taken with the head of the patient at a 90-degree angle to the table. To change the position and direction of the sagittal plane. To return the plane to its original position. Therefore it is possible to adjust the position of the sagittal plane to account for this. Cut Cut Menu file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. 2D and 3D measurements will be off. d.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. you can adjust the properties of the cutting path by clicking on the Properties button. After drawing. select the corresponding option from the Simulation Cut menu. The following window will appear and your cursor will change in a pencil. With this pencil you can draw your cutting path in 3D or in 2D.Import Page 132 of 169 There are two different cutting tools available: Cut Orthogonal to Screen and Cut with Polyplane: Cut with Polyplane To launch the cut with polyplane tool.htm 2/3/2014 .

htm 2/3/2014 .Import Page 133 of 169 The cutting path will be visible in 3D and in 2D (if the option "Contour Visible" is selected) Functions on Objects to Cut Visible Lists if the object is visible or not by means of glasses. Click on the glasses to file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

Click on the glasses to change the visibility of the cutting path. Lists if the contour of the cutting path is visible or not by means of glasses. Cut with Curve By defining a contour on the 3D object you can make more complex cuts. Functions on Cutting Paths New Properties Allows you to create a new cutting path. To launch the cut with curve tool. You can also define if the cutting path should be closed or not.Import Page 134 of 169 change the visibility of the object. Contour visible Lists if the contour of the object is visible or not by means of glasses. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 . the original objects will be kept. You can also change the angle of the cutting path by left-clicking and dragging the red arrow on the cutting path. The following window will appear and your cursor will change in a pencil. Show only selected objects Keep originals If the keep originals checkbox is checked. Displays the properties of the selected cutting path: In this properties dialog you can change the depth. The Preview button can be used to preview the adjusted cutting path before applying the changes. Click on the glasses to change the visibility of the contour of the cutting path. Makes the selected objects visible and the unselected objects invisible. otherwise they will be deleted and only the cut objects will remain. thickness and the extensions at the front and the end of the cutting path. Click on the glasses to change the visibility of the contour of the object. Cutting paths can be adjust after their creation by left-clicking on the points of the cutting path and dragging them. Visible Contour Visible Lists if the cutting path is visible or not by means of glasses. select the corresponding option from the Simulation Cut menu.

the original objects will be kept.htm 2/3/2014 . Deletes the point of the cutting line that was drawn last. Makes the selected objects visible and the unselected objects invisible. otherwise they will be deleted and only the cut objects will remain. a red line will appear on the 3D that represents your cutting line. Show only selected objects Keep originals If the keep originals checkbox is checked. You can still adjust the control points therefore over the mouse over the cutting path. A yellow line will appear which represents the extension of the cutting path. Sets the distance between the cutting line and its extension file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Lists if the contour of the object is visible or not by means of glasses. When you indicate the points. the object is now cut AND split at the same time. This extension can be adjusted in the main dialog box.Import Page 135 of 169 Indicate points all around the 3D object to indicate your cutting path. The cut will only complete when all extensions are floating above the 3D object. Functions on Objects to Cut Visible Contour visible Lists if the object is visible or not by means of glasses. When you hover over a control point the cursor will change into a cross with circle. Click on the glasses to change the visibility of the contour of the object. Closes the cutting line. You finish the cutting path by double clicking the left mouse button (or click once the right mouse button). To select this point click your left mouse button and drag the control point to its new location. Click on the glasses to change the visibility of the object. After you’ve checked the extensions click OK. Make sure that the extensions aren’t crossing the 3D object. Functions on Cutting Lines Indicate Close Delete Last Extensions Shows the indicate tool and enables you to indicate a cutting line.

Import Page 136 of 169 Cut Orthogonal to Screen To launch the cut orthogonal to screen tool. Click on the glasses to change the visibility of the object. Click on the glasses to change the visibility of the contour of the object. Lists if the contour of the object is visible or not by means of glasses. Show only selected objects file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.htm 2/3/2014 . Makes the selected objects visible and the unselected objects invisible. The following window will appear and your cursor will change. select the corresponding option from the Simulation Cut menu. You have to select an object to cut from the list before you can preview or apply the cut. Functions on Objects to Cut Visible Contour visible Lists if the object is visible or not by means of glasses.

Import Page 137 of 169 Keep originals If the keep originals checkbox is checked. Split To launch the split tool. only the largest part or only the two largest parts. otherwise they will be deleted and only the cut objects will remain. Closes the cutting line. Click on the glasses to change the visibility of the contour of the object. The following window will appear: Functions on Objects to Split Visible Contour visible Lists if the object is visible or not by means of glasses. otherwise they will be deleted and only the cut objects will remain. you always need a cut first (with the cutting tool) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. If the keep originals checkbox is checked.htm 2/3/2014 . To split. Lists if the contour of the object is visible or not by means of glasses. all cut parts. Functions on Cutting Lines Indicate Close Delete Last Shows the indicate tool and enables you to indicate a cutting line. the original objects will be kept. Click on the glasses to change the visibility of the object. Makes the selected objects visible and the unselected objects invisible. select the corresponding option from the Simulation menu. Show only selected objects All parts Largest part Two largest parts Keep originals This way you can choose which parts you want to keep. the original objects will be kept. Deletes the point of the cutting line that was drawn last.

Reposition To launch the reposition tool.htm 2/3/2014 .Import Page 138 of 169 Then you select which object you want to cut and press the "Preview" and or the "Apply" button. select the corresponding option from the Simulation menu. The following window will appear: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

If the option ‘Move with Mouse’ is enabled. select the object(s) you want to reposition. Y and Z axis by grabbing one of the colored rotation handles. Click on the glasses to change the visibility of the object.you can move the object around in all views. the original objects will be kept. You can also rotate the 3D around the axis perpendicular to the camera view by grabbing the outer ring of the rotation tool. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Rotation handles will be shown on the 3D object. Makes the selected objects visible and the unselected objects invisible.Import Page 139 of 169 Objects to reposition Selection of the Object to be repositioned First. Click on the glasses to change the visibility of the contour of the object. Translation and Rotation Objects can be translated and/or rotated. If you grab the center of the box -marked by a yellow rectangle. Lists if the contour of the object is visible or not by means of glasses. If the keep originals checkbox is checked. To change the rotation center grab and move the middle of the tool. select the ‘Rotate with Mouse’ options. You can rotate the 3D object around the X. To rotate an object. Functions on Objects to Reposition Visible Contour visible Show selected only Keep originals Lists if the object is visible or not by means of glasses. otherwise they will be deleted and only the cut objects will remain. Move with mouse Objects can also be manipulated using the mouse. By clicking on one of the arrows you can move the 3D object along an axis. The values of translation and rotation are shown in the statusbar. For each type of manipulation the measure can be adjusted to suit your needs. a box and arrows will appear around the object in both 3D and 2D views.htm 2/3/2014 .

Select the points you want to use from this list. following dialog will appear for each selected point: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. you can move landmark points that are located on the surface of a 3D object and the 3D object will then automatically be moved according to the new position of the landmark points. you can do this in the Anthropometric Analysis tool.htm 2/3/2014 .Import Page 140 of 169 Restrict DOF Several restrictions on the manipulation of an object can be chosen. Possible restrictions are: translating over axis. When you click on the Registration button. you will see a list of all the indicated landmark points. When you click on the OK button. Registration With the registration function. rotating over an axis and rotating over a point. Off course unrestricted manipulation is also an option. translating over plane. If you have not created any landmark points.

htm 2/3/2014 .Import Page 141 of 169 In this dialog you can move each point by specifying a Lateral. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. It is possible to save a position and to afterwards easily return to that position. The home position of the object can always be reached by clicking on ‘Go to Home Position’. the new position of the 3D object will be calculated and the 3D object will be moved to that position. Vertical and Rostral placement. When you click on the OK button. Switching/saving Positions A few buttons are available in this step in order to facilitate the object manipulation. Motion Analysis An analysis overview of the motion will be displayed if you click on the Analyze Motion button.

For this.Import Page 142 of 169 Finishing the reposition If the repositioning of the objects matches the situation you want to achieve. you can click ‘finish’. select the corresponding option from the Simulation menu. Place Distractor To place a distractor. you first need to cut and split. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. You can place a distractor on an existing object or on a part of an object.htm 2/3/2014 .

Import Page 143 of 169 By selecting 'Place Distractor' from the Simulation menu the following window will appear: Functions on Objects to place the distractor on Visible Contour visible Lists if the object is visible or not by means of glasses. A distractor library will appear in which you can chose which distractor you want to place. After selecting the distractor from the library the following window will appear: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Click on the glasses to change the visibility of the object. Click on the glasses to change the visibility of the contour of the object. Lists if the contour of the object is visible or not by means of glasses. Select on which part you want to place your distractor and click "Next".htm 2/3/2014 . Show selected only Makes the selected objects visible and the unselected objects invisible.

Reposition with Distractor To launch the reposition tool. the second mouse click determines the point of the distractor on the moveable part of the bone.htm 2/3/2014 . select the corresponding option from the Simulation menu. You can also change the vector of the distractor by left-clicking on the red arrow originating from the distractor and dragging the arrow. The first click determines the point of the distractor on the fixed part of the bone.Import Page 144 of 169 Locate the distractor with two mouse clicks in the 3D view. Functions on Objects to Reposition with the distractor Visible Lists if the object is visible or not by means of glasses. The distractor can also be aligned to the sagittal or axial slices or to the Frankfurt plane. Click on the glasses to change the visibility of the object. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Adjust the Distractor Position The direction of the distraction vector can be adjusted with the following window.

resp. Makes the selected objects visible and the unselected objects invisible.htm 2/3/2014 . Note.Import Page 145 of 169 Contour visible Show selected only Lists if the contour of the object is visible or not by means of glasses. that an analysis can only be made of you have first saved the position you wish to analyze. The default translation for each step will be 1mm but this can be change by editing the field in between the two translation buttons. The total translation of the distractor is shown underneath the translation buttons. Wizard Osteotomy Wizard file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. using a distraction measure that is too large will simply put the distractor in its starting. To translate the distractor simply use the ‘-’ and ‘+’ buttons. it is not possible to move a distractor beyond its starting or ending position. ending position. Click on the glasses to change the visibility of the contour of the object. The home position of the object can always be reached by clicking on ‘Go to Home Position’. It is possible to save a position and to afterwards easily return to that position. Translating according to the Vector of the Distractor After you have selected the object to be repositioned you will be able to use the ‘Translate distractor’ option. Switching/saving Positions A few buttons are available in this step in order to facilitate the object translation. Analyze Motion An analysis overview of the motion will be displayed if you click on the ‘Analysis Overview’ button. however. Of course.

a number of predefined conventional procedures are available: LeFort I conventional. but take into account that the cutting paths within the wizard are simplified.htm 2/3/2014 . select the corresponding option from the CMF/Simulation menu. If none of these suite your needs you can also opt for a custom planar or a custom freeform cut. If you opt to perform an osteotomy via the wizard. Click Next to proceed. LeFort II. To launch the Osteotomy Wizard.Import Page 146 of 169 The Osteotomy wizard will guide you through all the necessary steps to come to a good simulation. LeFort III. Some conventional options you can choose from are available. Selecting the object(s) to cut To select the object you wish to cut simply place a mark in the column before the object you wish to cut. Multiple file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Each step will exactly tell you what needs to be done before you can go on to the next step. Step 1: Choosing the type of surgery In the first step of the osteotomy wizard you must indicate the type of surgery you are about to perform. simulation becomes easy and fast. Step 2: Select the objects and indicate landmarks a. If you select a surgery a short description will appear in the bottom pane of the window. Genioplasty. Sagittal split and Ramus lengthening. LeFort I trapped. Like this.

The landmarks will appear in the cephalometric window at the right side of your screen.Import Page 147 of 169 objects can be selected. If you have previously done a cephalometric analysis some or all landmarks may have already been indicated. Visibility of the object(s) To take a better look at the object(s) you have selected it may be useful to hide all other objects in the 3D view. click on the ‘Show Selected Only’ button. b. if you want to retrace your steps in the wizard you can always use the ‘Back’ button.htm 2/3/2014 . When all landmarks have been indicated the ‘next’ button will no longer be disabled and you can continue the wizard. To continue the wizard click on ‘Next’. you need to select the mandible as object you want to cut in. Example: when you want to perform a simulation of a sagittal split surgery. Indicate the appropriate landmarks The wizard will ask you to indicate the landmarks that are appropriate for the type of osteotomy you have chosen. To achieve this. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA.

click on the ‘Show Selected Only’ button. d. Adjusting cutting path dimensions Besides manipulating the cutting path position. Step 4: Splitting the 3D objects This step of the wizard will guide you through the cut itself. a. height and width. To achieve this.Import Page 148 of 169 Step 3: Adjusting the cutting path This step allows you to manipulate the cutting path that was loaded from the library to make it perfectly adjusted to the patient’s 3D model. Adjusting cutting path position When cutting an object it is important to make sure the cutting path cuts through the entire object. Planes can either be translated or can be rotated. If all objects that need to be cut are selected. To achieve this it is possible to adjust the position of the cutting plane. You can change its thickness.htm 2/3/2014 . Object(s) before split Between step 3 and 4 a copy of the object(s) you selected to be cut has been made. click on the ‘Split’ button. The cutting path can be seen and adjusted both in 2D and 3D. Enable the ‘Show contour’ option and the path will be made visible on the 2D images. For both operations a measure of adjustment can be assigned to allow for easy. c. Of course it is also possible to reset the cutting plane to its original dimensions. fast and accurate manipulation. Displaying cutting path in 2D CT views It may be helpful to see the location of the cutting path on the axial and sagittal views. Object visibility To take a better look at the object(s) you are working on it may be useful to hide all other objects in the 3D view. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. it is also possible to adjust its dimensions. These objects are visible in the ‘Objects before Split’ pane. b. It is at this stage still possible to deselect one or more of the objects. a.

simply select the object in the pane and click on ‘Remove Selected’. You can make it visible again by clicking on the box with the color of the original object in the 3D view toolbar. These will also be visible in the 3D view. the newly created objects will appear in the ‘Objects after Split’ pane. at this stage in step 4 you are able to choose to make an additional cut. This option will restart the wizard. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The original object still exists. It is also possible to remove one of the new parts that have been created. but will be hidden in the 3D view.htm 2/3/2014 . c. Step 5: Repositioning the 3D objects After having done the cut. To do this.Import Page 149 of 169 b. Objects after split After the split. you can reposition one or more of the newly obtained parts. Make additional Cut If you need to make more than 1 cut. Off course any motion can be easily analyzed.

If the object that disappeared in the 3D window is the object you want to reposition. Make the object visible again by clicking on the b. Selection of the Object to be repositioned In the same fashion as you have done in the previous steps. If the option ‘Move with Mouse’ is enabled. the cursor will change into a rotation sign and you will be able to rotate the object around its center. a box will appear around the object in both 3D and 2D views. select the object(s) you want to reposition. Repositioning the selected Object There are two ways of repositioning an object: with the using the keys or using the mouse. This too is possible in both 2D and 3D views.htm 2/3/2014 .you can move the object around in all views. To rotate an object. Using the mouse Objects can also be manipulated using the mouse.Import Page 150 of 169 a. Note: You can check if you selected the right object by clicking on the . For each type of manipulation the measure can be adjusted to suit your needs. grab one of its corners. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Using the keys Objects can be either translated or rotated. If you grab the center of the box -marked by a dot. you selected the right object.

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c. Restrict the Degrees of Freedom

Several restrictions on the manipulation of an object can be chosen. Possible restrictions are: translating over axis, translating over plane, rotating over an axis and rotating over a point. Off course unrestricted manipulation is also an option. The rotation/translation point, axis or plane needs to be indicated by the use of the cephalometry. Once these point are indicated, and after selection of a restriction, you need to select them in the following window (for example when you choose “rotate around an axis”):

Click OK, select the object you want to reposition, and only the restricted movement will be enabled.

d. Registration The registration option allows you to easily reposition objects using landmarks. Click on ‘registration’ and select the landmarks you want to reposition.

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After clicking ‘ok’, SimPlant will take you through all the points you have selected and allow you to reposition them and the objects they are associated with.

e. Switching/saving Positions A few buttons are available in this step in order to facilitate the object manipulation. It is possible to save a position and to afterwards easily return to that position. The home position of the object can always be reached by clicking on ‘Go to Home Position’.

f. Motion Analysis An analysis overview of the motion will be displayed if you click on the ‘Analysis Overview’ button. Note, however, that an analysis can only be made of you have first saved the position you wish to analyze.

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Finishing the Wizard
If the repositioning of the objects matches the situation you want to achieve, you can finish the wizard.

Distraction Wizard
The distraction wizard will guide you through all the necessary steps to come to a good simulation. Each step will exactly tell you what needs to be done before you can go on to the next step. Like this, simulation becomes easy and fast, but take into account that the cutting paths within the wizard are simplified. If you opt to perform a distraction via the wizard, a number of predefined conventional procedures are available: alveolar, unilateral ramus, bilateral ramus and maxillary distraction. If none of these suite your needs you can opt for a freeform way of simulating a distraction (see later).

To launch the Distraction Wizard, select the corresponding option from the CMF/Simulation menu.

Step 1: Choosing the type of surgery
In the first step of the distraction wizard you must indicate the type of surgery you are about to perform. Some conventional options you can choose from are available. If you select a surgery a short description will appear in the bottom pane of the window.

Click Next to proceed.

Step 2: Select the objects, choose your distractor and position it in the 3D window

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a. Selecting the object To select the object you wish to cut simply place a mark in the column before the object you wish to put the distractor on. Example: when you want to perform a simulation of a unilateral distraction, you need to select the mandible as object you want to cut in.

b. Visibility of the object To take a better look at the object you have selected it may be useful to hide all other objects in the 3D view. To achieve this, click on the ‘Show Selected Only’ button. To continue the wizard click on ‘Next’, if you want to retrace your steps in the wizard you can always use the ‘Back’ button.

c. Choose the distractor from a library Distractors are available from Martin, Synthes and Medicon. If the distractor that you would like to use is not available in the distractor list, please contact Materialise and we will do our best to add this distractor to the library. To choose your distractor, select it and click OK.

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d. Locate the distractor and align After selection of a distractor your cursor will change into a pen. You can locate the distractor now with two mouse clicks in the 3D window. The first mouse click needs to be on the fixed part of the bone, the second mouse click on the part that will be distracted.

Once the distractor is indicated, the distractor can be translated or rotated and the vector can be aligned according to your needs. To translate the distractor, move your cursor over the distractor in the 3D window. When you get the symbol , you can translate the distractor by using your left mouse button. When you get the symbol you can change one of the distractor points (the fixed or the moveable one) by using your left mouse button. To rotate your distractor, you can use the available keys in the wizard dialog box.

To align the vector of the distractor, you can use the available keys in the wizard dialog box, or you can use the direction arrow. By moving your mouse to the top of the arrow, and left clicking, you can drag the arrow (the vector) towards the desired direction.

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e. Indicate the appropriate landmarks

The wizard will ask you to indicate the landmarks that are appropriate for the type of distraction you have chosen. The landmarks will appear in the cephalometric window at the right side of your screen.

If you have previously done a cephalometric analysis some or all landmarks may have already been indicated. When all landmarks have been indicated the ‘next’ button will no longer be disabled and you can continue the wizard.

Step 3: Adjusting the cutting path
This step allows you to manipulate the cutting path to make it perfectly adjusted to the patient’s 3D model. The cutting path can be seen and adjusted both in 2D (if you check ) and 3D.

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a. Object visibility To take a better look at the object(s) you are working on it may be useful to hide all other objects in the 3D view. To achieve this, click on the ‘Show Selected Only’ button. b. Adjusting cutting path position When cutting an object it is important to make sure the cutting path cuts through the entire object. To achieve this it is possible to adjust the position of the cutting plane. Planes can either be translated or can be rotated. For both operations a measure of adjustment can be assigned to allow for easy, fast and accurate manipulation. c. Adjusting cutting path dimensions Besides manipulating the cutting path position, it is also possible to adjust its dimensions. You can change its thickness, height and width. Of course it is also possible to reset the cutting plane to its original dimensions. d. Displaying cutting path in 2D CT views It may be helpful to see the location of the cutting path on the axial and sagittal views. Enable the ‘Show contour’ option and the path will be made visible on the 2D images.

Step 4: Splitting the 3D objects
This step of the wizard will guide you through the cut itself.

a. Object(s) before split Between step 3 and 4 a copy of the object(s) you selected to be cut has been made. These objects are visible in the ‘Objects before Split’ pane. It is at this stage still possible to deselect one or more of the objects. If all objects that need to be cut are selected, click on the ‘Split’ button.

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b. Objects after split After the split, the newly created objects will appear in the ‘Objects after Split’ pane. These will also be visible in the 3D view. The original object still exists, but will be hidden in the 3D view. You can make it visible again by clicking on the box with the color of the original object in the 3D view toolbar.

It is also possible to remove one of the new parts that have been created. To do this, simply select the object in the pane and click on ‘Remove Selected’.

Step 5: Repositioning the 3D objects
After having done the cut, you can reposition one or more of the newly obtained parts. Off course any motion can be easily analyzed.

a. Selection of the Object to be repositioned

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In the same fashion as you have done in the previous steps; select the object you want to reposition.

Note: You can check if you selected the right object by clicking on the . If the object that disappeared in the 3D window is the object you want to reposition, you selected the right object. Make the object visible again by clicking on the

b. Repositioning the selected Object You can only reposition the object according to the vector and the position of the distractor. Click the + key to see the movement of the object.

c. Switching/saving Positions A few buttons are available in this step in order to facilitate the object manipulation. It is possible to save a position and to afterwards easily return to that position. The home position of the object can always be reached by clicking on ‘Go to Home Position’. ‘Go to end position” shows the maximum distraction of that particular distractor device.

d. Motion Analysis An analysis overview of the motion will be displayed if you click on the ‘Analysis Overview’ button. Note, however, that an analysis can only be made of you have first saved the position you wish to analyze.

Finishing the Wizard

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If the repositioning of the objects matches the situation you want to achieve, you can finish the wizard.

Soft-tissue
3D Soft tissue simulation is an extra module on top of the CMF module. An extra password is needed to activate this tool. Once activated, you can find a new menu item in the CMF/Simulation menu, namely “Soft Tissue”.

After you simulated the maxillofacial surgery with the Simulation functions (osteotomy or distraction), you can check how the soft tissue will change according to the new bone positions.

To launch a new soft tissue simulation, select the corresponding option from the Soft Tissue menu.

The following window will pop up, and the 3D objects in the 3D window will disappear.

First select the postoperative hard tissue objects. The ones you select will also become visible in the 3D window.

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Note: For optimal results of the soft tissue simulation, the spine should be included as hard tissue. If the spine is not segmented, you can go to the segment module (if you have SimPlant Pro) and segment in a very easy way the spine.

Then select the pre operative soft tissue object. The selection will become visible in the 3D window.

Click next and the soft tissue simulation will start calculating. A progress bar shows you how long the calculation will take.

Note: The calculation time depends on the performance of your computer and the size of the data. It can range from a few seconds to a few minutes.

Once the calculation is completed, the soft tissue simulation will appear on your screen. To see the simulation, click the “Play” button. The speed of the animation can be adjusted by using the Speed bar.

Advanced tools

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Merge
To launch the merge tool, select the corresponding option from the Simulation menu. The following window will appear:

Functions on Objects to Merge
Visible Contour visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object. Makes the selected objects visible and the unselected objects invisible.

Show only selected objects Keep originals

If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain. To merge, you always need select two or more 3D objects or STLs. The selected objects will then be merged to one STL by clicking on the Ok button.

Mirror
To launch the mirroring tool, select the corresponding option from the Simulation menu. The following window will pop up:

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or a split part. left-click three times in any 2D or 3D view. A plane will then be constructed through those three points. Functions on Mirror planes Allows you to indicate a new plane. Click on the glasses to change the visibility of the contour of the object. the original objects will be kept. Show only selected objects Keep originals If the keep originals checkbox is checked. You can mirror a complete part of the bone. New file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. otherwise they will be deleted and only the cut objects will remain. Click on the glasses to change the visibility of the object. Makes the selected objects visible and the unselected objects invisible.Import Page 163 of 169 Functions on Objects to Mirror Visible Contour visible Lists if the object is visible or not by means of glasses.htm 2/3/2014 . Lists if the contour of the object is visible or not by means of glasses. This can be checked in 3D and in 2D. To do this.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. press Apply. With the preview button you can check the result. Then select a mirror plane or create your own by clicking on the New button and indicating three points of the plane in 2D or 3D. If the result looks ok.htm 2/3/2014 .Import Page 164 of 169 Select the part you want to mirror.

The result of the rescale operation will be put in the 3D Objects list. Click on the glasses to change the visibility of the object. To launch the boolean tool.Import Page 165 of 169 Boolean The boolean tool allows you to do a boolean operation (Minus. Click on the glasses to change the visibility of the contour of the object. select the corresponding option from the Design menu. Unite or Intersect) between 3D Objects. STLs or MedCAD Spheres and Cylinders. To launch the rescale tool. Lists if the contour of the object is visible or not by means of glasses.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. select the corresponding option from the Design menu. Rescale The rescale tool allows you to rescale 3D Objects or STLs. Makes the selected objects visible and the unselected objects invisible. The following window will pop up: Functions on Objects to Boolean Visible Contour visible Lists if the object is visible or not by means of glasses. otherwise they will be deleted and only the cut objects will remain. the original objects will be kept. Show only selected objects Operation Keep originals The boolean operation you want to perform on object 1 and 2. If the keep originals checkbox is checked. The result of the boolean operation will be put in the 3D Objects list.

Lists if the contour of the object is visible or not by means of glasses. Uniform Keep originals If the uniform option is selected. Show only selected objects Factor Size You can choose the rescale factor in X. The following window will pop up: Functions on Objects to Rescale file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Click on the glasses to change the visibility of the contour of the object. Makes the selected objects visible and the unselected objects invisible.htm 2/3/2014 . Click on the glasses to change the visibility of the object. If the keep originals checkbox is checked.Import Page 166 of 169 The following window will pop up: Functions on Objects to Rescale Visible Contour visible Lists if the object is visible or not by means of glasses. select the corresponding option from the Design menu. You can also give in a size in X. otherwise they will be deleted and only the cut objects will remain. Y and Z direction. Y or Z and the rescale factor will be calculated automatically. The size field displays what the size of the object will be in X. To launch the smoothing tool. the original objects will be kept. Y and Z direction with the specified factor. Y and Z direction. The result of the smoothing operation will be put in the 3D Objects list. Smoothing The smoothing tool allows you to smooth 3D Objects or STLs. the rescale factor will be the same for X.

the shrinkage of the object due to the smoothing will be countered. The smooth factor determines how much smoothing is performed. to be part of the same plane that contains the selected triangle. Click on the glasses to change the visibility of the contour of the object. Lists if the contour of the object is visible or not by means of glasses. Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. The Edge Angle-value defines which angle should be used to determine edges of the part that cannot be removed.Import Page 167 of 169 Visible Contour visible Lists if the object is visible or not by means of glasses. select the corresponding option from the Design menu. The result of the triangle reduction operation will be put in the 3D Objects list. Show only selected objects Iterations Smooth factor Compensate shrinkage Keep originals You can choose how many smoothing iterations will be performed. Makes the selected objects visible and the unselected objects invisible. an Edge based triangle reduction or an Advanced Edge based triangle reduction. If the compensate shrinkage setting is enabled. The Tolerance indicates the maximum deviation in mm that a related triangle may have. To launch the triangle reduction tool. Triangles deviating less than this angle will be grouped into the plane of the other triangles. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The following window will pop up: Functions on Objects to Rescale Visible Contour visible Lists if the object is visible or not by means of glasses. Show only selected objects Reducing mode Tolerance Edge Angle You can choose between a Point based triangle reduction.htm 2/3/2014 . otherwise they will be deleted and only the cut objects will remain. If the keep originals checkbox is checked. Click on the glasses to change the visibility of the contour of the object. the original objects will be kept. Makes the selected objects visible and the unselected objects invisible. Triangle Reduction The triangle reduction tool allows you to do a triangle reduction of 3D Objects or STLs. Click on the glasses to change the visibility of the object.

The cursor will change into a pencil. Note that this is only a representation of the nerve channel as you have drawn it. Draw a nerve This function allows you to draw the nerve. While drawing the nerve you can scroll through the images with the cursor keys and follow the nerve channel if needed. click your left mouse button to add a point. Nerves toolbox This tool allows you to create a representation of nerves. Each time only the relevant buttons are enabled in the toolbox. The points of a selected nerve are in white. you need to click (press and release the left mouse button) once to define the course of the nerve. connected by an interpolated line. Remove a point from a nerve file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. Add a point to a nerve Click on the add point to nerve button. Fine adjustments can be made by dragging the points to a new location. Start drawing the nerve: for every change in direction along the nerve. The nerve is drawn manually and consists of a series of points. The action you do is always performed on the selected nerve.htm 2/3/2014 . The points of a non-selected nerve have the same color as the lines of the nerve. double click the left mouse button or click the right mouse button. hover the mouse over the nerve segment were you want to add the point. The nerves toolbox will appear on the screen.   Select a nerve Select the cursor tool and click on a nerve to select it. In order to terminate the nerve.Import Page 168 of 169 Iterations You can choose how many triangle reduction iterations will be performed. The cursor will change to a pencil. Delete a nerve Select the nerve you want to delete and click on the Delete nerve button. Select the nerve icon from the tools toolbar or select the Tools menu and then Draw/manipulate nerve. These are the steps to perform:   Select the Create nerve tool. The nerve can be moved entirely by dragging the orange line. Close the toolbox by clicking on the black cross in the top right corner or by clicking again on the nerve button in the tools toolbar.

Show the list of nerves Click on this button to display the Nerves tab on the project management.Import Page 169 of 169 Click on the point of the nerve you want to delete. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh58AA. The selected point will be colored green. Click on the Remove point from nerve button to delete the point.htm 2/3/2014 .

If you wish to try that section of the tutorial and you don’t have the required module(s) installed.html and register.htm 2/3/2014 . Chapter 7: FEA Tutorial Tutorial that shows how to use the FEA module. This is very important when setting a threshold and when you use the Profile Line function. surf to http://www. In this tutorial we will discuss three topics:    How to do an Automatic Import How to organize images How to do a Semi-Automatic Import Note: To import images from a tape you need to use the Dump Tape function Note: There are 3 ways to import images. Chapter 3: Simon Tutorial that shows some advanced segmentation functions to remove artefacts. Note: In Mimics you have the possibility to use both Hounsfield and Grey Values. To download the tutorial files from our website. RP Slice or MedCAD). Chapter 9: CFD Tutorial Tutorial that shows how to use the FEA module for linking to CFD.Mimics Tutorial Page 1 of 79 Mimics Tutorial In Mimics. Copy the demo files to this working directory.materialise. you can set a general default working directory (Options > Preferences). The extra tutorial files are a self-extracting zip-file. To switch between these two possibilities. only two of the files used in this tutorial would be put in the MedData folder.com/software/download_ENG. You can then choose Mimics and then the link for Tutorial Datasets. Chapter 5: Obturator Tutorial that shows how to make a mold of a cavity by segmenting the soft tissue around the cavity. Make sure that you have read and write permissions in this directory. an evaluation period of that module can be obtained on request. All the other ones can be found on the CD or from our website. when the format of the files is known to Mimics  semi-automatic. Bitmap or Tiff images  manual import (Case 6). If you have chosen to install the demo files during the Mimics installation procedure. go to Options > Preferences. To unpack the file. Chapter 1: Import Chapter 2: Mimi Import The goal in the first part of this chapter is to teach you how to import images and convert them into a Mimics project. The second part will illustrate how to organize the images in the project you made.g. when the file type is unknown and you need to specify some parameters manually file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. General tab and select the Pixel unit you want to use. Most tutorials need one or more modules of Mimics (STL+. double click on it and choose your MedData folder as destination folder. Chapter 6: Manual Import Tutorial that shows how to use the manual import function. The following tutorials are available: Tutorial that shows how you can import images in Mimicis Tutorial that shows how to do a basic segmentation and 3D calculation. Chapter 8: Simulation Tutorial Tutorial that shows how to use the Simulation module. Chapter 4: Hip Tutorial that shows how to use the MedCAD module. e. depending on their format:  automatic import.

An Import Project Wizard will be displayed where you can select where the images to be imported can be found (STEP 1). orientation parameters.Mimics Tutorial Page 2 of 79 Automatic import To start the Import wizard. After clicking on the Next button you will reach the second step of the Import Project Wizard. Note: If you want to keep all the files. In this window some information about the project can be found. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. In the import wizard. A list of files will be displayed in the Filename column and all the files will be automatically selected. you have to perform a manual import (see Case 6).htm 2/3/2014 . first select File and then choose Import Images. press the Next button. pixel size. If this happens. If you click on the displayed containing the correct path and format of the images. etc. you can select the images and press the Next button. If the format of the images is known to Mimics (see the general help files for a list of known formats). button. patient name. Click the Next button. such as the number of images. This selection can be done in two different ways: either you can click on the first file and then on the last one you want to include while keeping down the Shift button (this way you will include all files in the interval) or you can select the files one by one while keeping down the Ctrl button. browse to the MedData folder and select the folder called “Import1”. an import message will be Note: In this case the file type is recognized. in which you need to select the studies to be converted. otherwise first change the selection of images to fit your needs. The study you have just imported is already selected by default. but in some cases the message log tells you that one or more images are of an unknown file type.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.htm 2/3/2014 .Mimics Tutorial Page 3 of 79 Now you can click the Convert button and you will see a progress bar during the conversion process. the project will be opened automatically displaying the Change Orientation window since one or more of the orientation strings were missing in the original images.

Move the mouse cursor to the top X in the sagittal or coronal image. Edit. Note that all the other orientation strings are completed automatically. a menu appears with all possible orientation strings. you can decide to exclude some images if they are not good or if you don’t need all of them. Select “Top”. go to File and then choose Organize Images. The cursor shape changes to a hand and if you right-click. If the orientation of the images is right you can click OK and your Mimics project will be opened. To access the Organize Images window.mcs that don’t include parts of mandible or that don’t contain any information. etc.. Now you can process your images using the tools explained in the tutorials dealing with Case 2 and Case 3 (Threshold. we can decide to delete the images of the project Simon. Actually if you look at the axial image you see the orientation strings L and R. Region Growing.Mimics Tutorial Page 4 of 79 Now you need to set the Orientation Parameters that were missing and change the ones that are incorrect. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. For example.) Organizing images Once you have opened your project. which stand for Left and Right respectively together with A and P which stand for Anterior and Posterior. In the coronal and sagittal image two red Xs are displayed instead of the above mentioned orientation strings.htm 2/3/2014 .

the red mark will disappear and the image will be unchecked in the list on the left. On closer inspection you can also notice that the image at table position –1.htm 2/3/2014 . You can now save your Mimics project with the name “Organizing Images. you should not see the ones you unselected.5 is the last one that contains information about the mandible. a new window will be displayed.5 do not contain any information about mandibular bone. Again select File > Import Images and browse to the \MedData\Import2\ directory. If you look at the images you will notice that the ones that correspond to table positions –49.5 and –48.mcs” going to File and then Save As. All the consecutive images will be unselected also.5 and choose Unselect after this. Press OK and scroll through the axial images to check if the correct ones are visible in the project. After you have done this you can make a segmentation following the next tutorial (Case 2) Semi-automatic import Now we will try to import the Bitmap images you can find in your MedData directory in the "Import2" subdirectory. If you press the Next button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. So you can click on these two images to unselect them.Mimics Tutorial Page 5 of 79 First of all you can get a better look at the images changing the preview size to Medium or Large by clicking on the arrow on the left side. Right-click on the image at position –1.

Now the import continues in similar a similar way to the automatic import. The topics that will be discussed are:          Opening the Project Windowing Thresholding Region Growing Creating a 3D representation Displaying a 3D representation STL+ Procedures Generating a STL file RP Slice procedures file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. This information should be collected by someone who is familiar with the machine used to make the CT-Scan.Mimics Tutorial Page 6 of 79 The only information you need to provide/change is the slice distance and the pixel size. You will need to select the study you wish to convert and your Mimics project will be created after clicking on the Open button. Now you should be able to set the orientation parameters as described in the previous paragraph and calculate a good 3D. Mimi In the second case of this tutorial we will show you some basic features of Mimics.htm 2/3/2014 . It is very important to insert the exact values since the dimensions of the volumes and the 3D depend on them. If the data is accurate. you can press OK to continue with the second step of the Import Project Wizard.

htm 2/3/2014 . If you need to change the orientation of a view. The upper left corner is a reslice of these images in the xz-direction (xzview or coronal view) and the bottom left is a reslice in the yz-direction (yz-view or sagittal view). The view on the right shows the images as they are exported by the scanner (xy-view or axial view). The Open dialog box shows all projects in the working directory. All images are loaded and displayed in three views.Mimics Tutorial Page 7 of 79    Generating a contour file Generating supports View of the end result Opening the project From the File menu. The different colors of the intersecting lines (dashed lines) refer to the colors of the contour lines of each view so every line refers to the slice in the corresponding view. go to File > Change Orientation. select Open (Ctrl+O). file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. You can easily navigate through the images by clicking on any point of the CT images in any view: the intersecting lines will move crossing each other in the point you clicked and all the views will be updated showing the corresponding slices. This will open a window in which you can change the orientation parameters simply by clicking on it with the right mouse button (see tutorial Case 1). Double click on the mimi.mcs file (Mimics project file).

The gray values in between the window will be mapped on a shade of gray.htm 2/3/2014 . Windowing First of all. You can also choose one of the predefined “windows” by selecting the appropriate scale from the menu on the bottom of the tab.masks. e. Usually several masks will be needed to obtain a final segmentation object that contains the information that is needed. all images are correct. This action can be performed at any time. each displayed with their own identifying color. You can change the contrast in the corresponding tab of the Project management. however. Thresholding Thresholding means that the segmentation object (visualized by a colored mask) will contain only those pixels of the image with a value higher than or equal to the threshold value. The contrast tab shows the histogram of the project with a line representing the “window”. In the right border of the window you will see a slider that allows you to scroll through the images from the active view. All gray values above the end point of the line will be displayed in white. brain tumor. One can create several dependent or independent .Mimics Tutorial Page 8 of 79 Every indicator can be turned off by selecting View > Indicators in the Menu Toolbar. Contrast enhancement is a very good tool for selecting parts with different intensities. If. bone vs. You can change the window size by clicking your left mouse on one of the points and dragging it to its new location. To move the window select the line and drag it to its new position. For example: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. go to File > Organize Images. There you can add or remove images (see tutorial Case 1). Sometimes an upper and lower threshold is needed. you have an image set from which you want to remove some images. In our current project (Mimi). The following steps will describe the necessary actions to achieve a nice segmentation mask. The gray values or Hounsfield units below the start point of the line will be displayed in black. the segmentation mask contains all pixels between these two values.g. we have to adjust the contrast of the images displayed in the different views. A segmentation mask is a collection of pixels of interest that constitute an object you wish to work on.

release for zooming. a lower threshold value is recommended since this results in a model with less holes. If you want a good visualization model. The threshold value is displayed in the Min. only the very dense parts remain selected. Click the left mouse button on the image and drag for . If your model will serve for modeling prostheses. First. If a proper threshold is set. select the project management button in the main toolbar. select it in the mask tab in the project management. Some tips for selecting an adequate threshold value: Look at different images. In a project you can have different masks but you can use the segmentation tools only on the active mask. Click the Zoom-button : the mouse is displayed as a loupe. Zoom in on a part you’re interested in. creating a zoom rectangle. After the thresholding operation a green mask will be created. the page up and page down keys using the slider on the right in the window border moving the slice indicators . select Box. To end thresholding. Click the Threshold button . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Using both an upper and a lower threshold is needed when the nerve channel needs to be selected. click the Unzoom-button A good threshold value for Mimi is about 270 (Hounsfield scale).Mimics Tutorial Page 9 of 79 A low threshold value makes it possible to select the soft tissue of the scanned patient. box of the Threshold toolbar. On the other hand. select a threshold slightly above the intensity plateau of the soft tissue. press the left mouse button on a slider in the Threshold Toolbar and move the slider by moving the mouse (while still holding the left mouse button). from the pull-down menu next to the zoom button. Click the Profile button Draw a line (with your mouse) in the main window. click the Apply button. Along this line an intensity profile is generated (figure 2-1). place the line between the soft tissue plateau and the top value of the bone. With a high threshold. The straight horizontal line is your current threshold value. In case the project management isn’t active. If you just want a nice looking model. Defining a good threshold value also depends on the purpose of the model. click on End Thresholding to save the current value. To choose the active mask. To return to the whole image. Click on Start Thresholding and drag the straight-line up/down to set a good threshold. You can change images of any view by:    using the arrow keys.htm 2/3/2014 . when the model serves for modeling prostheses a higher threshold value is preferred. To change the threshold value.

Clicking on the green glasses will hide the green mask. To make this new mask active. Now. but after a month. you still know that the Yellow mask contains the skull. when you reload a project. The new segmentation is colored yellow. Selecting one mask will make it active. since all previous work is lost after changing the threshold value. Click the left mouse button on one point in the green area of the object of interest (which is a part of the current segmentation object. Therefore. i. The mouse is now cross-shaped and the Region Select the Source (= Green) and Target mask (= New Mask). it may be interesting to rename the mask (in Project Management. It’s time to build a 3D representation. Check the mask on different images. Click on the name Yellow so that it becomes editable. or press Ctrl + R. The program starts to calculate the new segmentation. Masks tab). When we check the images. it might be difficult to know in which mask your end result was stored. part of the skull). Clicking the button again will make the green mask visible. Click the Close button to close the Region growing window. replace Yellow with a more telling name like ‘skull’. The names of these masks are Green and Yellow.e. Region growing The region growing tool makes it possible to split the segmentation created by thresholding into several objects and to remove floating pixels. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Click the Region growing button Growing window is on the screen. we see that everything looks fine.htm 2/3/2014 . select "Yellow" in the Visualization toolbar.Mimics Tutorial Page 10 of 79 You can also hide any mask by clicking on the glasses of the corresponding color. Note: Thresholding needs to be done before region growing. all points in the current segmentation object that are connected to the marked point will be used to form a new mask. Creating a 3D representation In the mask tab you see all created masks listed with their respective threshold.

Mimics Tutorial Page 11 of 79 Click on the Calculate 3D button . It will take the place of the In the vertical 3D toolbar on the right. to display the 3D representation. click the 3D button coronal images (left corner at the bottom). To do so. like skull and teeth. like Top. This is only the visualization on the screen. by clicking on the button window zoom with the buttons or Pan with the on the right of the   change the color of your model and background by clicking the right mouse button and selecting the option “Color” . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. You can in The model can also be displayed transparent. Once the 3D image is loaded. the less time the program needs to calculate the 3D image and the less memory is needed to load the 3D image afterwards. Here you can mark (with a green dot in the column called “Selected”) which masks you want to visualize and calculate the 3D by clicking on the Calculate button (if you made segmentations of different objects.htm 2/3/2014 . different operations are available:  rotate the model with the button button on the right of the window or moving the mouse pressing the right  select different standard views. The "Calculate 3D Models" Dialog box is displayed. this parameter doesn’t need to have any impact on the model that you will actually build on an RP machine!!! Of course. Front. by clicking on the glasses. push the Toggle Transparency button switch between different degrees of transparency (high-medium-low-opaque) by clicking the square button the transparency column. you can calculate them together and go to lunch in the mean time). Displaying a 3D representation If you are in 3-panes layout. the lower the quality. you can set the visibility of the different calculated 3Ds. You can set the visualization quality of your model. Bottom. This can also be done in the Project Management's 3D Objects Tab. Select "Skull" from the list.

the file appears in the output area. Fill in the appropriate values like in the dialog box and click the Finish button. STL+ procedures The intermediate file between Mimics and STL+ can be one of the following:    “. Generating a STL file Click the Next button: the Conversion to STL Dialog box is displayed. After clicking the Save button the . The calculation starts and an STL file is generated. If you're interested in creating files for Rapid Prototyping or exporting an STL or VRML file. This step is not always necessary. Choosing the 3D tab would have enabled you to select a 3D object. select the mask called “skull” and click the Add button. If you wish.Mimics Tutorial Page 12 of 79 To change the background color.htm 2/3/2014 . Press the STL+ button and a window will pop up on the screen with 3 different tabs for each option.3dd” file Masks 3D Objects You can create a skull. Calculation of the machine files can be done directly on the masks or on 3D objects.3dd file and pressing the Add button. go to View > 3D Background Color and select the color you prefer. you can rename the output file to “skull” (in the same way as you would in Windows Explorer). like STL or VRML. please continue this tutorial. You can use the parameters as they are displayed in the screenshot. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Choose the Masks tab. Click on the STL+ button in the Masks Tab of the project Management. there are different possible formats.3dd files will be placed in the MedData folder.3dd file by clicking the Export 3dd button in the Project Management’s Masks Tab or with the option Export > 3dd in the main toolbar. Please note that multiple 3Ds or masks can be selected and added to the list but it is not possible to add both masks and 3Ds. Depending on the type of output file format. Further details about these parameters can be found in the STL+ Reference guide. After selecting the mask or the . Select the output format.

Masks tab and choose the RP Slice button. Within the RP slice dialog you are able to generate a contour file from a mask or a 3dd and you can also generate a support file from a contour file.htm 2/3/2014 . the Conversion to RP format Dialog Box is displayed. The file generated in this tutorial will be used in the RP Slice procedures. the mask will appear in the area below. Click the Next button. Choose the mask called “skull” from the list in the Masks tab of the RP Slice window that just opened and press the Add button.Mimics Tutorial Page 13 of 79 RP Slice procedures RP Slice procedures Note: It is also possible to generate slice files for Stratasys machines. You can use the following parameters in the RP Slice Parameter dialog box. Instructions on how to use these files in Quickslice are also provided (read the STL+ Reference Guide). Generating a contour file Go to Project Management. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Select the SLI Output format.

Mimics Tutorial Page 14 of 79 Click the Next button to proceed.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Fill in the values as displayed below. the Calculation Parameters dialog box is displayed.

the calculation starts and an SLI file is generated. Click the Finish button. Contour files tab and set the .Mimics Tutorial Page 15 of 79 Further details about these parameters can be found in the STL+ Reference guide. Go to the RP Slice window. Select the file you created in the previous section and press the Add button.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.SLI file option in the Input format field. Generating supports For building the object with Stereolithography. a support is generated directly from the slice file with RP Slice module . For calculating the support structures. please continue this tutorial.

Mimics Tutorial Page 16 of 79 When one contour file is selected. the Next button in the “RP slice – Mask/3dd/contour file selection” window opens the window displayed below.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.

good luck with the building of the model !! View of end result file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. a support till layer height 50.htm 2/3/2014 . The program defaults to full height.Mimics Tutorial Page 17 of 79 Note: It is also possible to generate slice files for Stratasys machines. In the case of "Mimi".00 is sufficient (depending on the resin used). You now have a model and support file. they certainly need support. To prevent that these islands start floating during the building process. Press the Finish button to start the support generation. Check the slices from bottom to top and search for new ‘islands’. This isn’t always necessary. Instructions on how to use these files in Quickslice are also provided (read the STL+ Reference Guide). so that the whole model is supported. an SLI file is created.

file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.htm 2/3/2014 . The mandible of the patient was partially edentulous and needed a prosthesis. The topics that will be discussed are:   Opening the Project Preparation of the data o o o o o o o   Windowing Thresholding Region growing Editing Artifacts Multiple particles Scan prosthesis Boolean Operations View of the end result Opening the project In the File menu. select Open (Ctrl+O).mcs file. a scan prosthesis was made that resembled the new teeth to be implanted.Mimics Tutorial Page 18 of 79 Simon The Simon case is an example of a dental segmentation. First. well positioned against each other. Double click the Simon. The result is that you see both the bone and the prosthesis in one image. It will be your job to do the segmentation of the mandible and the prosthesis. Such a procedure with a scan prosthesis gives better esthetic results and the surgeon is able to make a better planning. Because scan prostheses are made out of barium sulfate. The patient had this prosthesis at the correct position in his mouth during the CT scan. The images in the Simon project are CT scans of the jaw together with the scan prostheses. they are clearly visible in a CT image. an opaque material.

at position -30. Profile line over the bone (upper image) and the corresponding profile dialog box file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Press Start thresholding and drag the threshold line to a value of about 538 (Hounsfield scale). The figure below shows a profile line and the corresponding profile dialog box.htm 2/3/2014 . Thresholding Go to an axial image where the mandible (without the teeth) is visible (for example. 50).Mimics Tutorial Page 19 of 79 Preparation of the data Windowing For correct windowing see the windowing procedures in "Mimi" (Case 2). Close the dialog box. End the thresholding and save your settings. Press the Profile line button and draw a line over the bone.

we will still have to edit the images and make sure that all the pixels that belong to the mandible are really in the mandible mask.Thresholding Separating maxilla and mandible To separate the mandible from the maxilla. one for the mandible and another for the maxilla. In figure below. The skull is now added to a new mask. Make sure you don’t forget any! Go to a lower image in the data set and do a region growing of the mandible (do not activate the Leave Original Mask option). so we have to find the best possible position. Editing . Make the previous mask invisible (make sure the skull mask is active before making the first mask invisible). In this case you can’t do the region growing again from the same original mask.Mimics Tutorial Page 20 of 79 Region growing Press the Region Growing button and click on the bone of the skull to start the region growing. In the corresponding axial image all pixels have to be removed from the active mask. But be careful! Because it was not possible to perform the separation 100% correct. If the result of the region growing is not satisfying. Then we perform a region growing on the mandible. The result is that both mandible and maxilla will be in a different mask and thus separated. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Note: In the region growing toolbar. The position of the axial image corresponding to the position of the horizontal indicator in the figure above. is -4. double click the name of the mask and change it to “skull”. Note that it will not be possible to separate them completely in every image. we have to disconnect them manually.50. you still have the complete original mask and you can start over. choose a big square as type of cursor and remove all pixels from the active mask. Look at the sagittal image and place the horizontal indicator between the maxilla and the mandible. if you activate the Leave Original Mask option. the pixels selected with region growing will be put into a new mask. these two masks are shown and the red line in between indicates the layer that was removed from the active mask. Now you have two masks. The trick we will use is the one explained in the Obturator case (Case 5) further on in this tutorial.htm 2/3/2014 . If this option is not activated. the pixels selected during region growing are removed from the original mask. In the Masks tab. We first erase a layer from the active mask somewhere between the mandible and the maxilla. Click on the Project Management icon . Select the Erase mode. but they will also remain in the original mask. Go to this image and press the Edit masks button . Change in the Project Management the name of the two masks to “mandible” and “maxilla” respectively.

50 that some pixels (at the left side in the image) from the maxilla are wrongly put in the mask of the mandible? Move both indicators until their point of intersection indicates the wrong pixels (figure above). belonging to a tooth of the maxilla. mark these pixels with the indicators as it is done in the figure below. In the axial image.Mimics Tutorial Page 21 of 79 Scroll through the coronal images and check if every pixel that belongs to the mandible is in the proper mask.htm 2/3/2014 . move the indicators again in the coronal image so their intersection points to the wrongly colored pixels. Two layers belong to the maxilla mask and the other layer is the one we erased in the beginning to make the disconnection. It concerns two layers of pixels. Do you notice at position 64.25 (or the coronal image at position 43. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.50). In the sagittal image at position 87. because that tooth is also indicated with the point of intersection of the indicators (figure below).50 and 5. you can be sure you erased the whole tooth from the mandible mask. erase the tooth from the mask of the mandible. You cannot be mistaken. In the two corresponding axial images (position -6. But now it’s the opposite situation! Three layers of pixels that belong to the mandible are not in the mandible mask.50. remove the pixels that are indicated by the indicators from the active mask.25) another collection of badly masked pixels is visible.50): the indicators point out the tooth that does not belong to the mandible mask. Axial images (position: left -5. If not. right -6. If the two layers of pixels are shown in grey values in the coronal image. Again.

To set a different local threshold. You can check this very easily by looking at the sagittal or coronal image: if the wrongly masked layers (figure 3-6) now have the color of the mandible mask it’s alright. will be added to the active mask. otherwise you’ve forgotten some pixels. When you move the square over the image while pressing the left mouse button. all the pixels that already belonged to the active mask and that don’t have a grey value within the range will be removed from the mask. i. press Enter. Indicators point to pixels that should belong to the mandible mask (sagittal view). The local threshold range For the moment we don’t have to change the threshold values. After you changed the value. but it will be used later on in this case to remove artifacts out of the image.htm 2/3/2014 . the box with the two default threshold values is shown on your screen. With the draw mode. We will make use of a local threshold to do this. The threshold mode (ctrl + T) is used to set a local threshold. but there is one more condition before they are really added: their HU values must lie in the range shown in the box (figure 3-7). Press the left mouse button and go over the tooth with your cursor.Mimics Tutorial Page 22 of 79 In the corresponding axial images (at positions -4. This means that if you apply a local threshold in a particular area of one image. The Edit toolbar shows up and the threshold mode is already selected. With the threshold mode you do the same. In this case. On the other hand. Now we can say that the whole mandible is in the mandible mask. When you activate this mode. To make this threshold clear.50 and -3. Press Ctrl + T. just press E (or select the Erase mode with your mouse) and erase them. that’s true. Choose a circle as type of cursor and make it more or less the same size as a tooth. this threshold doesn’t apply to the other images in the project. draw. Make sure you got the tooth completely. it’s much safer to add pixels by taking into account their grey values. but there is a difference! With the draw mode you add every pixel you touch with your cursor. Make sure that the mandible mask is the active mask.50) the pixels (of a tooth) should be added to the mandible mask. Local threshold: In the obturator case it is mentioned that there are three modes to choose from in the Edit toolbar. If you repeat the thresholding in the necessary axial images (see before to know their positions) you should become a sagittal image like in the figure below. Maybe you now wonder why we will add the pixels of the teeth that belong to the mandible with this local threshold method and not with the draw mode we will use in the obturator case.e.50 and -2. can’t you also add pixels to a mask? Yes. erase and threshold. Suppose you added too much pixels. Remark that the threshold we’ve set in the beginning of this case was global and it applied to every image in the dataset. a short intermezzo is inserted below. press one of the two arrow buttons and double click on a threshold value. every pixel that comes to lie within the square and has a threshold in the threshold range you just set. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Our segmentation will be more accurate.

To enter the Edit mode. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. don’t panic. Change this value to 3000 (if you are working in Hounsfield Units) and press Enter.Mimics Tutorial Page 23 of 79 Sagittal image after local thresholding Artifacts The images still don’t look nice. If you removed the edges from the mask. Go with your cursor over the artifacts and notice that they disappear. The threshold mode is already selected. Because the Hounsfield Units of the artifacts are lower than the ones of the teeth. Click on the top arrow of the threshold range box (figure 3-7) and double click the threshold 1 value. but not the default one like we just used to add the pixels. this is the way you should work. Set the threshold range back to the default one by clicking once on the lowest arrow and move your cursor over the tooth again to restore the edges. Scroll through the axial images and remove all the artifacts from the mask of the mandible. You get the message that the mask consists out of multiple parts. their pixels will remain in the mask. The artifacts in the left image are removed with a local threshold. because of all the artifacts. So. press Ctrl + T. if you accidentally go with your cursor over the teeth. except for the edges (their HU are lower). The right image shows the result Multiple particles Let’s calculate the 3D image of the mandible. Press the Calculate 3D button and select the mandible mask to be calculated (choose low quality).htm 2/3/2014 . We are going to get rid of them by again performing a local threshold. Answer with “Yes”. Moreover. So by setting a very high threshold the artifacts will be removed from the mask because their grey values are not in the range. Why do we use this high local threshold? Because the HU values of the artifacts are lower than the ones of the teeth.

once at either side. because sometimes in 2D it looks like there is no connection. That caused the message you got about the multiple parts. You can delete the first 3D (with the particles) listed in the 3D tab of the Project Management. There are two ways to achieve this. Scan prosthesis Can you distinguish between the natural teeth and the scan prostheses in the 3D model of the mandible? It’s quite simple. To avoid this you have to do a region growing before calculating the 3D. In the figure below. The second option is to perform a segmentation of the prosthesis. Keep the following advice into account: remove enough pixels in the surrounding of the prosthesis. we first have to make sure that the prosthesis is completely disconnected from the natural teeth. Press the 3D view button again to get back the sagittal image. We opt for the latter. Press the Region growing button and click into the mandible. but there is still one in 3D. There are 3 teeth of the scan prostheses at the patient’s left side and one at his right side. The goal is to get the prosthesis nicely isolated in every image.htm 2/3/2014 . So a 3D model can be very tricky! file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. the scan prosthesis (axial view) is marked with rectangles. But. Now calculate and visualize the 3D model of the final mandible. Axial image indicating the prosthesis in the boxes. The intention is to remove (from the final mandible mask) the pixels surrounding the prosthesis and the pixels connected to the prosthesis. We will do a region growing of the prosthesis twice. the natural teeth are connected to the bone. Change the name of this new mask to “Total mandible”. The first one is to proceed with the segmentation of the final mandible and to remove the prosthesis from the active mask. We would like to have the mandible without the prosthesis and the prosthesis itself into two different masks. The particles are due to the editing you’ve done to remove the artifacts. Rotate the model and remark that there are little particles floating around the mandible. while the scan prostheses are not.Mimics Tutorial Page 24 of 79 Visualize the 3D by pressing the 3D button.

Also in the layers where you don’t see the prosthesis it can be useful to remove some pixels belonging to the teeth next to the prosthesis. The last one will be used later on to perform Boolean operations. That’s nice. If you think you disconnected the prosthesis completely. the left prosthesis and the right prosthesis in three different masks. In the figure below it is shown for the axial image at position 11. delete the last mask in the list (generated for the region growing) and remove more surrounding pixels from the backup mask. Let's use the following calculation: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. This last option is very important! The prosthesis is disconnected in this layer Click on the left or the right prosthesis.htm 2/3/2014 . make the previous mask active again. Make sure your target mask is a new mask (if not. repeat these actions for the prosthesis at the other side. Scroll through the axial images and remove (enough!) pixels surrounding the prosthesis from the active mask. If this is not the case.50. but we said earlier that we would like to have the mandible without prosthesis. press the Color button in the masks tab and choose the color you like). while the original Final mandible mask is left unchanged. This way a backup mask is created that we can use to do the segmentation of the prosthesis.Mimics Tutorial Page 25 of 79 Project Management – Masks tab Make the mask of the final mandible active and press the Duplicate button in the Masks tab of the Project Management window. only the prosthesis should be shown in the color of the target mask. Give the masks of both prostheses proper names. press the Region Growing button. Proceed with this backup mask (if you don’t like the color. If you disconnected the prosthesis entirely. Boolean Operations Let’s examine what we’ve obtained so far: the final mandible (with prosthesis). select “new mask” from the drop down list) and that you activate the Leave Original Mask option. We can achieve this with some Boolean operations we can achieve this. Press the Boolean operations button .

press the Apply button. View of end result Hip In the fourth tutorial we will discuss some of the possibilities of the MedCAD module. Mask A: mask C (obtained in the first step) Operation: minus Mask B: right prosthesis Result: new mask  After these options are set. press the Apply button. The topics that will be discussed are:   Opening the Project Preparation of the data file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Press the Close button. Show also the left and right prosthesis. You should have a model that looks like this one.Mimics Tutorial Page 26 of 79 Mandible without prosthesis = total mandible – left prosthesis – right prosthesis Follow the steps below:  Mask A: final mandible Operation: minus Mask B: left prosthesis Result: new mask (called mask C for reference) After these options are set. The other 3Ds can be set invisible. The last mask (the one that should be active now) contains the pixels of the mandible without the prosthesis.htm 2/3/2014 . Calculate and view the 3D of this mask. To finish this tutorial you will have to have a license for the MedCAD module.

Click the left mouse button on one point of the right femur (left on the images).htm 2/3/2014 . Check the Multiple layer box. The 3D view will replace the sagittal view. select the yellow mask and press the Calculate 3D button. In the File menu. In this IGES-file a basic reference system calculated on the data as well as a partial modeling of the outer contours using freeform surfaces will be present. The right femur has now been grown into a new mask (Normally if you have started fresh the femur will be in the yellow mask now). Double click the hip. It is strongly advised to first follow the tutorial of Case 2 to obtain the necessary skills for segmentation and image processing. Therefore use the following steps:    Click the Region Grow button or press Ctrl + R. The yellow mask will be automatically selected in the Calculate 3D window. Calculation of the Polylines Go to the Project Management. go to Project Management. The procedure is explained in more detail in Case 2. The Open dialog box shows all projects in the working directory. Masks tab. Set this threshold in your base mask and apply it. Preparation of the data Thresholding A good minimum threshold value for this case is 1235 (Grey Values) or 211 (Hounsfield values). To calculate your 3D. select Open (Ctrl+O). file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.Mimics Tutorial Page 27 of 79 o o     Thresholding Region growing Calculation of the Polylines Patching of the contours Creation of MedCAD objects Visualization possibilities Opening the project The objective for this part is the creation of a file ready to use in all CAD-systems supporting the IGES-interface. Region growing We want to make a model of the right femur (left in the image set). You can find more details about this in Case 2.mcs file (Mimics project file). The part of the "Hip" we’ll focus on is the right femur of the patient (left in the images). but you need to set the quality to “high” and press the Calculate button. Set the Source to Green (if this is your base mask) and Target to New Mask.

You can also calculate polylines by clicking the button in the segementation toolbar. 3D view of the polylines Patching of contours Since we are only interested in the outer contours. Go to layer -523 and zoom in on the right femur in the 2D image (xy plane). you should see something like the image below. The Create Polylines dialog box appears with the Yellow mask already checked. When you rotate the polylines and switch on the depth shading (check box in the bottom part of the screen). select the Calc Polyline option from the action list. The borders of your yellow mask will be calculated and displayed as a polyline in both 2D and 3D images.Masks tab Select the yellow mask and click on the action button. Click the Polyline Growing button in the MedCAD toolbar.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Now you will only see the polylines. press the 3D View button. click OK. Make the 3D invisible by clicking on the yellow cube in the right toolbar. To see them in 3D. In 2D you can see the polylines right away: they're displayed together with the images and your masks.Mimics Tutorial Page 28 of 79 Project Management . we need to select these out and grow them to a new set of polylines.

the polyline growing can continue. Hold the left mouse button down.. Do a Polyline Growing from Selection 1 to a New Set . In order to select a polyline.. Similar editing and updating of the polylines needs to be done on slices: -483 till -479. Don't forget to update for every image.. the set that will contain the grown polylines. Go back to layer -485 and perform the Polyline Growing (from Set 2 to Selection 1. You can delete this set by selecting it in the Project management and then pressing the Delete button.e. matching parameter 95 %. -471 (on the femur head). keep in mind that it will be the yellow contours that will be updated. Auto Multi-Select on) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. be sure to turn Auto Multi-Select off. Next the polylines need to be updated and then we can proceed with the polyline growing:   Click the Edit masks button and go to the erase mode or press Ctrl + E Make sure that the Yellow mask is Active    Erase the extension on the bone Press the Ctrl + U key or the Update Polylines button in the Edit toolbar Repeat this for the following images. Image –485 of the Hip At this slice you see a cavity in the contour. Lose the cavity by drawing in the mask and updating the polyline (Ctrl + U). you need to draw a rectangle over it. Select the polyline. Scroll to image –485 (figure below). This needs to be removed in layers –513 and -511. When all corrections have been made. drag it to the opposite corner of the rectangle and then release the left mouse button.Mimics Tutorial Page 29 of 79 Set all parameters as displayed in the image below: i. -475. the set to start from. The growing of the polylines stopped at layer -513 because of a small extension on the bone (scroll through the images pressing the Ctrl + Arrow keys). .htm 2/3/2014 . Scroll back to image -513 and click the Polyline Growing button. Set "selection 1" as the target polyline and use 96 % as matching parameter. . If you want to restore this with editing. so we need to remove the pink polyline first.

htm 2/3/2014 . The end result should look like the figure below. The following dialog box will appear. The femur head and the greater trochanter will be grown into new selection sets. Polyline sets Creation of MedCAD objects On the great trochanter and on the lower part of the femur we will fit a Free Form Surface. In the Project Management on the Polylines tab. on the femur head.Mimics Tutorial Page 30 of 79 When all editing was performed properly. all layers until -477 are now stored in Selection 1. you will find a button Fit Surface. we will fit a sphere. Choose Selection 1 and press the Fit Surface button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.

To fit a Sphere on Selection 2.Mimics Tutorial Page 31 of 79 Surface Fit Parameters You can accept these default values and a Free Form Surface will be fitted on Selection 1. The basis of a B-spline is a polynomial and a polynomial has the tendency to wave. Repeat this set on Selection 3. Choose the correct polyline set. The Free Form Surfaces are visible in 3D as a shaded surface and in 2D you will see a cross-section on every layer of this Free Form Surface. if the number of points is too high. go to the MedCAD menu and select Sphere > Fit on Polylines.htm 2/3/2014 . The result of all these fittings should look like following figures: Objects fitted on the Polyline sets Imported STL files file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. the fit on the polyline will become worse. Note: Some caution in increasing the number of control points is advised. So.

. Click the Load. Such a model can be used as a mold for obturator prostheses. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Both actions can be performed in 2D as well as in 3D.htm 2/3/2014 . Obturator In the previous cases we have segmented bone structures. In order to protect the tissue weakened by irradiation and to be able to breathe and eat normally. The topics that will be discussed in this tutorial are:   Case Study Preparation of the data o o o    Editing Region growing View of the end result Windowing Orientation Thresholding Case study Obturator prosthesis for oncologic patients Case presented by Dr. One can rotate and move this prosthesis to obtain the best fit of the prosthesis onto the femur and check the design related to the bone structures. This way the region of interest is captured in a 3D box delimited by the removed layers. An interesting application is the modeling of the soft tissue around the cavity of the mouth. The STL file will be visible both in 2D (as cross-sections) and in 3D.Mimics Tutorial Page 32 of 79 Visualization possibilities When a prosthesis is designed. button. To adjust the position of the STL file. Visch from Daniel den Hoed Kliniek Rotterdam. click the Move button to move the STL file or the Rotate button to rotate it. Next we perform a region growing that starts in the region of interest..L. You can import an STL file in the Project Management from STLs tab. Because this region is separated from the active mask. By erasing one layer from the active mask in every direction. How are we going to model this soft tissue? Since we are only interested in the area around the cavity. The first picture shows the cavity in the mouth of the patient after resection of a tumor. the cavity and the soft tissue around it will be separated from the rest of the image. we need to limit the model to the region of interest. whereas in this project we are going to make a softtissue model. From the new mask a 3D model can be calculated which will contain just the cavity of the mouth and the soft tissue surrounding it. L. only this area will be put into a new mask after the region growing is done. the STL file can be loaded in Mimics. In the case study following this introduction we will do just that. this hole needs to be filled by an implant.

it can be implanted very easily. These traditional techniques produce a master of the obturator prosthesis by making an impression of the cavity in a deformable plastic material.htm 2/3/2014 . As the silicone prosthesis is plastic deformable. The implant. Absolutely no surgery was needed to implant the obturator prosthesis. This model served as a direct mold for the implant. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. The soft tissue around the cavity.Mimics Tutorial Page 33 of 79 A CT-scan of the patient was made. was modeled. called an obturator prosthesis. clearly visible on the scans. The prosthesis fits the cavity much better than ever could have been achieved by using conventional impression techniques. was cast from the mold in a bio-compatible silicone.

Remark that all other orientation strings are completed automatically. Preparation of the data Preparation of the data In the File menu. a Change Orientation window pops up. Double click the obturator. Orientation When the project is loaded. select Open (ctrl+O) or click the button .Mimics Tutorial Page 34 of 79 The prostheses cast from such masters are always less accurate because of the presence of undercuts (the impression technique is not sensitive to local internal broadening of the cavity) and can severely damage the sensitive and vulnerable surrounding tissue. In the axial image you see the orientation strings L and R. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. a menu appears with all possible orientation strings. In the coronal and sagittal image several Xs are displayed instead of the orientation strings. This makes it possible to take it out for inspection and to replace it afterwards. which stand for Left and Right respectively. The cursor is changed to a hand and when you right-click. Windowing For correct windowing see the windowing procedures in "Mimi" (Case 2).htm 2/3/2014 .mcs project. Select “Top”. Do the same to set the Anterior-Posterior orientation parameter looking at the image displayed. The soft prosthesis is fixed by means of magnets on a hard dental implant. Move the mouse cursor to the top X in the sagittal or coronal image.

Press the Start thresholding button. going to File > Change Orientation. drag the lowest threshold line to the value –444 (Hounsfield scale). You can clearly see the transition from the soft tissue to the cavity. Press the Profile line button and draw a line in the axial image over the cavity. Profile line over the cavity of the mouth See the figure above (axial image on position 374) to have an idea where to place the profile line. You get a profile like shown in the image below.Mimics Tutorial Page 35 of 79 You can always change your orientation parameters. Press again the End thresholding button and answer yes to the question whether file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Thresholding A reliable way to define an appropriate threshold is to make use of a profile line (see also Case 2).htm 2/3/2014 . To visualize all the soft tissue in the mask.

will be added to the file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. this threshold doesn’t apply to other images in the project.Mimics Tutorial Page 36 of 79 you want to save the threshold value or not. To set a local threshold. Threshold (Ctrl + T): This mode is used to set a local threshold. After you have changed the value. When moving the square over the image while pressing the left mouse button. you add pixels to the active mask by going over the pixels with the square. go to Type and select a square from the drop down list. every pixel that comes to lie within the square and has a threshold within the threshold range you set. When the edit mode is not yet selected and you use the shortcuts between parentheses below. press one of the two arrow buttons and double click on a threshold value. The three modes available are listed below. Close the window. Notice that the length and the width of the square are displayed and can also be altered. Erase (Ctrl + E): This mode is the opposite of the draw mode. will get the color of your active mask. Your cursor has become a little square. a box with the two default threshold values is displayed on your screen. Press the Edit masks button .00. while pressing the left mouse button. go to position 387. If not.htm 2/3/2014 .   When you activate this mode. Editing In the axial image. just click in the little circle on the left of the mode or press the first letter of the desired mode. Remark that the threshold we’ve set in the beginning of this case was global and it applied to every image in the dataset. the edit toolbar appears and the associated mode is activated. press Enter. This means that if you apply a local threshold in a particular area of one image. The edit toolbar is displayed on your screen. In other words. To make a mode active. You remove all the pixels from the active mask by moving the square (keeping the left mouse button pressed) over the pixels in the image. The easiest way to change the size is to press the control key and your left mouse button simultaneously and to move to the right/left to make the square bigger/smaller.  Draw (Ctrl + D): Every pixel that lies within the shape of your cursor.

Working on the axial image in position 387 activate the Erase mode (Ctrl + E) and set a very large square (for example. Press your left mouse button and wipe off all the color in the image. Check both the Multiple Layer and Leave Original Mask checkboxes and click on an arbitrary position in the active mask. Close the region growing toolbar. You see that all the images at a position lower than 387. 200 by 200). the sagittal image is displayed and the arrow points to the layer that has been removed from the active mask (the slice indicator is moved down to see this). a window will be displayed on the screen.Mimics Tutorial Page 37 of 79 active mask. Select the axial image at a position lower than 387.00. Notice in the sagittal image that one layer is shown in grey values. all the pixels that were already part of the active mask and that don’t have a grey value within the range will be removed from that mask.htm 2/3/2014 .00 are put into a new mask (yellow mask in figure below). we will now perform a region growing . For the current case we are only going to use the draw and the erase mode. On the other hand. Be sure not to forget any pixels! Close the Edit toolbar. In the Simon case we already illustrated the threshold mode. (= the position of the image we removed from the active mask). To see the result of erasing the mask in one layer. In the figure below. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Press the Region Growing button.

we are going to erase a complete layer from the active mask on every side so that our region of interest is completely surrounded by these removed slices. To close our box. After we perform a region growing within that region.00 and press Ctrl +E (or press the Edit masks button and select the erase mode). Erase all pixels from the active mask at position 126. like we wanted. Activate the axial image. Try to visualize the situation and make sure you understand why we will now operate in the sagittal image. The top and the bottom of our box are now defined. To set the left and right boundaries of the box. Go to position 362. a region growing looks for pixels that are connected to each other and puts them into a new mask.htm 2/3/2014 . In figure 5-10 you can see the boundaries of the obturator on the yellow mask. Setting a boundary on the anterior side is not necessary. Two horizontal lines are shown in grey values. Make a big square and erase all the pixels from the active mask. we have limited the area of the region growing. In the axial image two vertical lines in grey values are visible.00 and 387. Take a look at the sagittal image. In the axial image the removed layer is visible. because we have disconnected the lower images from the higher ones. you have to remove two layers from the mask in the sagittal image. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.00. Activate the coronal image and remove all pixels from the active mask at position 76. But. Region growing Now that the box is delimited by the layers removed from the active mask. a region growing can be performed to get the obturator into a new mask. How will we proceed? In the same way as above. This is to make sure that the starting pixel for the region growing lies within the region of interest. we should have the oral cavity and the surrounding tissue in one mask. Press the Region growing button and click in the axial image within the box.49 (left boundary) and 42. Go to an axial image that has a position between 362. a separation still has to be made on the posterior side.Mimics Tutorial Page 38 of 79 Why are the images above this position not included into the new mask? As you already know.05 (right boundary) in the sagittal image.61. This will be the trick we will use to get our region of interest into a separate mask.

Choose custom quality and press the Calculate button.htm 2/3/2014 . Axial and sagittal view of the obturator Because we disconnected the pixels of the obturator from the other pixels in the original mask. Press the Calculate 3D button and select the mask of the obturator. The obturator is now within a new mask. In the figure below you clearly see the obturator within the active (blue) mask from the axial and the sagittal viewpoint. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. the region growing was confined to the region of interest. The processing of the 3D model is started.Mimics Tutorial Page 39 of 79 Boundaries of the obturator in the axial image.

If you press the bottom view you button.htm 2/3/2014 . make the axial image active and press the 3D View button .Mimics Tutorial Page 40 of 79 To visualize the 3D image. should obtain a model as shown in figure 5-12. Note that the model will always be visualized in the sagittal view. unless you select to view it in a fourth pane in Options > Preferences > Visualization > View. You can also enable transparency using the View of end result Manual Import In this case we will show you how you can use the manual import function to import any image data you want. Select Import Images form the File menu. The topics that will be discussed in this tutorial are:   Importing images Manual Import o o o  Parameters Preview the images Choosing the right parameters Convert the images Importing images The goal of this chapter is to teach you how to import images with the Manual Import option and convert them to a Mimics project. An Import Project Wizard will be displayed where you need to point to the "MedData\Import3" directory (STEP 1) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. On the right of the 3D object you see a toolbar and a button where you can select some predefined viewpoints for your 3D model .

htm 2/3/2014 .Mimics Tutorial Page 41 of 79 There are 3 ways to import images. Only the manual import will be explained in detail. Select the Manual Import button and press Next. depending on their file format: automatic. Note: When you press the Next button. The most important parameters are explained in the next paragraph. The images will be selected automatically. Manual import Manual import In the first step of the wizard. browse to the following path: \MedData\convert\. A new window is displayed on your screen. semi-automatic and manual import. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. all the project files listed will be converted. Select only the files you want to convert and leave the others unselected. because the other ways are more straightforward to use and are mentioned already in the tutorial Case 2.

htm 2/3/2014 . … The image is a matrix of pixels. the resolution of the images and the pixel type.Mimics Tutorial Page 42 of 79 Parameters File header size The file header size is calculated automatically. Typically a file contains both a file header and the image itself (in some rare cases also a footer is present). The file header can contain information about pixel size. Structure of a file Common sizes of images are: 256 * 256 file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. based on the file size. patient data. The horizontal (or vertical) image size is equal to the number of pixels in that direction.

the images have a resolution of 256*256.htm 2/3/2014 . What if you have a very large dataset? Don’t worry. fill in the number 2 for the interval. If you fill these values in. however. Press the OK button to close this window. Some examples of pixel types and their respective sizes (note that these types can be either signed or unsigned. If you want to know the amount of all the different grey values in the entire dataset (and not just in one image). the first of the 8 images is displayed. The default values for the other parameters are correct in this case. Exam information Fill in an appropriate name for the patient name. Preview the images Press the Show Preview button and take a look at the images to check whether the parameters we filled in were correct. This will be the name that is used for your project. Now only 4 images are taken into account.Mimics Tutorial Page 43 of 79 512 * 512 1024 * 1024 The number of bytes per pixel depends on the type of the pixel. Pixel properties Select Signed Short for the parameter Type and Low Byte First for the parameter Byte Swapping. On the left side. you have to press the Sample button on the right. Image information In the Image Information frame you see that the value for the image size is still 512*512. the third. this does not affect their size):     Byte: 1 byte Short: 2 bytes Long: 4 bytes Float: 4 bytes Image size = horizontal image size * vertical image size * number of bytes per pixel In this example. Correct the size to 256 * 256 pixels. For example. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. the fifth and the seventh image. you can restrict the amount of images that is used for this calculation. you will see that Mimics will set the file header size to 8432 bytes. Scroll through the images by moving the arrow on the right (or use your mouse wheel if you have one). namely the first. Notice that the title of the middle frame has changed to Sampled. For each image a histogram is displayed that gives you information about the range of grey values that are present in the image and their respective quantity.

Select the correct type and click the Update button to adjust the preview. Remark the loss of information due to the restriction to positive grey values.Mimics Tutorial Page 44 of 79 Choosing the right parameters Let’s experiment a little bit with the different parameters. Fill in the correct value and click the Update button to adjust the preview. Notice that all the pixels are shifted. Pixel Type: Select Unsigned Short for the pixel type and preview the images. Select the Show Preview button. Byte Swapping: Choose High byte first for the byte swapping and preview the images. because the data is read in the wrong order. Fill in the correct value and click the Update button to adjust the preview.   File header size: Set the file header size back to zero. You can see that there are local distortions all over the image.htm 2/3/2014 . The examples will help you fill in the right parameters when the image does not look like you expected it to.  Influence of the file header size Influence of the pixel type (signed/unsigned) file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.

In the Calculate 3D dialog select the High quality setting and click on calculate. The topics that will be discussed in this tutorial are:       Opening the Project Calculating a 3D Remeshing the 3D Exporting the remeshed 3D object Material Assignment Exporting the Volumetric Mesh Opening the project In the File menu. Browse to the directory where you have installed the extra Tutorial Files and double click the Femur. how to remesh the 3D and how to assign materials to the 3D.mcs file. Select the project you want to convert and check the box. We will start with a dataset of a Femur and explain how to do the segmentation.htm 2/3/2014 . FEA Tutorial In the FEA Tutorial we will explain the work-flow for making a FEA analysis on a model of the Femur. select Open (Ctrl+O). In the wizard window you should see the name of the patient and some other information about the data. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Press the Open button. how to calculate the 3D. The FEA and STL+ module have to be licensed to be able to conclude this tutorial. click the OK button in the Manual Conversion Options window. A Mimics project is created from the data and it will be opened automatically showing you the Change Orientation window. Calculating a 3D There is already a Green mask available in this dataset that will be used to calculate a 3D object. the project will be saved in the default folder (usually MedData).Mimics Tutorial Page 45 of 79 Influence of the byte swapping (high first/low first) Convert the images If the images look good in the preview.

select the calculated 3D and click on the remesh button. Start the remesher by going to the FEA menu and choose Remesh.htm 2/3/2014 .Mimics Tutorial Page 46 of 79 Remeshing the 3D In the next step we will remesh the 3D to make it optimal for FEA purposes. This will open the remesher with the part already loaded: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.

Mimics Tutorial Page 47 of 79 There are several quality parameters available to measure the quality of the triangles. For this example we will use the height/base parameter.htm 2/3/2014 . Make sure the Part Quality Sheet is on in the remesher (View menu: Part Quality Sheet): file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. This parameter measures the ratio between the height and the base of a triangle and normalizes the value. A perfect equilateral triangle has a quality of 1 and a very bad triangle has a quality of 0.

please have a look at the Remesher Help file. geometric error. In this case we have 170 triangles.e. 5. to a lesser degree. For more information about the remesher in general and quality in specific. Value 3 is the number of triangles that have a higher quality as our quality threshold.htm 2/3/2014 . Remeshing Protocol Below is a description of the remeshing protocol that you can use to remesh the Femur. Reduce the amount of detail Reduce the amount of triangles of your object Improve the quality of the triangles of your object Reduce the amount of triangles while preserving the quality Remove extra shells In between these steps measures will be taken to make sure that the object has no intersecting triangles and has no bad edges. 2. We will try to increase the quality of all those triangles. maximum triangle size and. STEP A: Because the 3D object will be used for FEA only. Since the minimum quality threshold is 0 in our project. The values given are those used for the Femur example and will have to be adapted if your part has a different scale (i. The protocol can be divided in three big steps: 1.Mimics Tutorial Page 48 of 79 This quality histogram shows the amount of triangles that have a certain quality. This is the quality threshold we will use for our project. there are 0 triangles with a lower quality Value 2 is the number of triangles that have a quality between the minimum and maximum threshold. 4.40. Below the histogram you can see three values:    Value 1 is number of triangles that have a quality below the minimum quality threshold. In this case 56618. you can reduce the amount of detail by applying a file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Then drag the green slider to 0. smallest edge length). 3.

STEP C: You can now optimize the quality of the triangles with the Auto Remeshing tool.htm 2/3/2014 .5 and 3 iterations. This tool uses parameters as the Min edge length and Max edge length. To reduce the amount of triangles. Go to Tools -> Smoothing (or select the smoothing icon toolbar). You can get an idea of the edge lengths present in the mesh by selecting the inspection parameter Smallest edge length and Largest edge length. angle 15 degrees. 5 iterations. once point-based and once edge-based. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.5.Mimics Tutorial Page 49 of 79 smoothing to the 3D object. go to Tools -> Global Remeshing -> Triangle Reduction -> Normal (or use the Normal triangle reduction icon on the top toolbar ) and use following parameters for the normal triangle reduction: geometric error: 0. Do this 2 times.1. on the top of the Perform a global smoothing and use the following parameters: Smooth Factor 0. In the Quality histogram select I to show the histogram of the selected inspection parameter. Shrinkage Compensation Factor 0. Step B: The 3D object contains too much triangles for an FE Analysis.

Max edge length 5 mm. STEP E: Call the self-intersection test.3. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Max Geometry error 0. minimal edge length 2. go to File -> Exit meshing module and click on Yes when the remesher asks you if you want to save the changes to the mesh.htm 2/3/2014 . To Auto Remesh the 3D object. make sure that the height/base parameter is selected as quality parameter. 3 iterations. No intersections should be found. number of iterations 3. STEP D : You can now reduce the amount of triangles while preserving the achieved quality of the mesh. Go to Tools -> Triangle reduction -> Qualtiy preserving and use the following parameters: Quality threshold 0. geometric error: 0.05 mm. You will then return to Mimics and the remeshed surface mesh can then be exported. preserve initial mesh on. Go to Tools -> Global Remeshing -> Auto Remesh Part -> Split-based Method (or use the Split-based remesh icon on the top toolbar ) and use the following parameters: quality threshold: 0. 1 move iteration.5.3. When you are satisfied with the quality of the mesh.Mimics Tutorial Page 50 of 79 You will notice that most of the triangles have a smallest edge bigger then 2mm and a largest edge bigger then 3mm. maximum edge length of 4 mm.1.

You can see the mesh listed in the FEA mesh tab. you can load this volume mesh in Mimics for material assignment. Abaqus or Ansys file. Browse to the directory where the tutorial files are installed and select the femur_volume_mesh. make it invisible. Patran. To load the volume mesh of the Femur go to the FEA menu and choose Import. This mesh is invisible by default. We have provided an example volume mesh for the Femur project which we will use. so make it visible. choose the correct format and export the mesh: This remeshed surface mesh can then be used to generate a volumetric mesh in your FEA preprocessor. Material Assignment When you have created a volumetric mesh in your FEA preprocessor from your remeshed object.out file. Abaqus and Ansys volume meshes are supported (see also supported files). It is of course also possible to use your own volume mesh of the jaw. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. To do this go to the FEA menu and choose Export. Select the 3D.htm 2/3/2014 .Mimics Tutorial Page 51 of 79 Exporting the remeshed 3D object Now you can export the remeshed 3D object in Mimics to a Patran neutral. If the surface mesh of the Jaw is still visible. We have provided a Patran neutral volume mesh in the tutorial files so this will be used further on.

so if you are working in Hounsfield units. We will use 10 materials for this tutorial. choose Preferences and change the Pixel Unit in the General tab. Choose Yes to continue. In this tutorial we will use the uniform method. After the calculation you will see following dialog box: Mimics shows for each grayvalue the amount of elements that were assigned that particular value.htm 2/3/2014 . STEP A: If the uniform method is not selected. You can see this discretization by choosing the Materials histogram: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.Mimics Tutorial Page 52 of 79 Note: We will use grayvalues for this tutorial. We will then convert this grayvalue to material properties. With the FEA mesh of the Femur selected. click on the Materials button. The FEA module will now divide the range of grayvalues that occur in the volume mesh into 10 equally sized intervals that each represent a material. Mimics will display a message that the grayvalues for this mesh have to be calculated before you can do a material assignment. please change this by going to the Options menu. click on the radio button next to Uniform. STEP B: Enter the number of materials in the edit box.

8 + 5925 * Density. STEP E: Check the values for the materials that will be assigned in the material editor: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. For this tutorial we will use following expression: Density = -13.4 + 1017 * Grayvalue. STEP D: Choose to write out only the E-Modulus material properties in the exported file by deselecting the selection boxes before Density and Poisson Coefficient.Mimics Tutorial Page 53 of 79 STEP C: Enter a density expression to convert the grayvalue of each material to a density. We will use following expression for the E-Modulus: EModulus = -388.htm 2/3/2014 .

The elements of the FEA mesh will be colored according to their materials: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.Mimics Tutorial Page 54 of 79 STEP E: Press the OK button to assign the materials to the FEA mesh.htm 2/3/2014 .

Mimics Tutorial Page 55 of 79 This volumetric mesh can then be exported together with the material assignment (in this case only the EModulus). Patran Neutral and Abaqus files and can then be used to do FEA analysis on the mesh. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Then go to the FEA tab.htm 2/3/2014 . To export the mesh go to the FEA menu and choose Export. add the correct mesh to the export list. together with the material assignment can be exported to Ansys. choose the required format and export directory and click on the OK button. Exporting the Volumetric Mesh The volumetric mesh.

how to calculate the 3D.Mimics Tutorial Page 56 of 79 Simulation Tutorial In the Simulation Tutorial we will explain some of the functions that are available in the Simulation module. split and reposition a custom implant. The Simulation module has to be licensed to be able to conclude this tutorial..htm 2/3/2014 . The topics that will be discussed in this tutorial are:          Opening the Project Windowing Thresholding Region Growing Calculating a 3D Cutting Splitting Mirroring Repositioning Opening the project file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. how to cut. We will start with a dataset of a skull with a hole in it and explain how to do the segmentation.

Press Start thresholding and drag the threshold line to a value of about 1250 (Grayvalue scale). End the thresholding and save your settings. Close the dialog box. The figure below shows a profile line and the corresponding profile dialog box. at position 18. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Thresholding Go to an axial image where the skull is visible (for example. Browse to the directory where you have installed the extra Tutorial Files and double click the Skull_with_hole. select Open (Ctrl+O). Windowing For correct windowing see the windowing procedures in "Mimi" (Case 2). Press the Profile line button and draw a line over the bone.htm 2/3/2014 . Profile line over the bone (upper image) and the corresponding profile dialog box Region Growing Now we will use the region growing tool to separate the skull from the artifacts and noise in the images:  Click the Region Grow button or press Ctrl + R.Mimics Tutorial Page 57 of 79 In the File menu.94).mcs file.

Check the Multiple layer box.  Click the left mouse button on one point of the skull. It is possible to hide/show a mask by clicking on the glasses. You'll see all created masks listed with their respective threshold. The skull has now been grown into a new mask. Selecting one mask will make it active and it will appear in the Active Mask field in the visualization toolbar automatically.Mimics Tutorial Page 58 of 79  Set the Source to Green (if this is your base mask) and Target to New Mask. Calculating a 3D Go to the Project Management by clicking its icon and choose the Masks tab. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.htm 2/3/2014 .

Cutting After the calculation of the 3D you will see a 3D representation of the Skull mask.Mimics Tutorial Page 59 of 79 Click on the Calculate 3D button. make the skull transparent by clicking on the button and choose to view the skull from the Right view. Now you can pan and zoom so you can see the hole clearly. Select the "Skull" mask if it is not already selected and click on the Calculate button. Here you can mark (with a green dot in the column called “Selected”) which masks you want to visualize and calculate the 3D by clicking on the Calculate button. you can clearly view the hole in the skull through the intact side. The "Calculate 3D Models" Dialog box is displayed. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. To be able to make a cut that fits well.htm 2/3/2014 . If you then zoom and pan.

The New button is already enabled so we can immediately start drawing a cutting path. double click with your left mouse button. Do this by clicking several times with your left mouse button around the hole like below.Mimics Tutorial Page 60 of 79 This way we can easily draw around this hole. To end the drawing.htm 2/3/2014 . select the Cut with Polyplane tool from the Simulation menu (CMF/imulation -> Cut -> With Polyplane). file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. To do this. You will see following dialog: Select the 3D from the skull in the Objects to Cut list.

You can now make the 3D opaque again by clicking on the not: button. You can then rotate the 3D to determine if the cut went through the whole skull or As you can see.htm 2/3/2014 .Mimics Tutorial Page 61 of 79 You can see that a cutting path has been added to the cutting path list. You can do this by clicking on the Properties button while the cutting path is selected. it would be best if we adjust the depth of the cutting path. This will open the cutting path properties dialog: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.

Enable the Keep Originals checkbox (since we want to keep the original 3D) and finish the cut by clicking on the OK button of the Cut with Polyplane tool. Select the freeform object. You can then click on Preview to preview the split and then on OK to apply the split.Mimics Tutorial Page 62 of 79 Adjust the Depth of the cutting path from 20. choose to keep all parts and disable the Keep Originals checkbox. When you are happy with the result.0mm to 30.htm 2/3/2014 . To do this. go to the CMF/Simulation Menu and choose Split. Click on Preview to view the result. Splitting The next step is to split the two cut parts of the newly generated 3D. close the Cutting Path Properties by clicking on the OK button. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. You can see in the 3D objects list that a new 3D object was added.0mm and enable the Closed checkbox (this will close the cutting path).

Mimics Tutorial Page 63 of 79 As you can see. choose Layouts and then Simulation Layout). Mirroring To mirror the part to the other side of the 3D. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Then make the original skull visible and go to the CMF/Simulation menu and choose Measure and Analyse . we will need a mirror plane. go to the Simulation Layout (by pressing F5 or by going to the View menu.htm 2/3/2014 . To do this. The Mimics simulation module generates a default sagittal plane. but we will have to adjust this plane a bit to make sure it's suitable for this dataset. You can make the largest part invisible since we will only need the small part to fix the defect in the skull. two different objects were created and have been given a different color.

htm 2/3/2014 . After this. Then mirror the part by going to the Simulation Menu. close the Measure and Analyse tool by going to the Simulation Menu and choosing Measue and Analyse again. Click on the Change button and adjust the Sagittal plane (by dragging the white points with your left mouse button) in the axial images to make sure the sagittal plane goes through the center of the nose. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.Mimics Tutorial Page 64 of 79 You can see in the right dialog that you can change the Sagittal Plane. Select the correct part and mirror plane and disable the Keep Originals checkbox and click on the OK button to apply the mirroring. from the advanced Tools select Mirror.

the part is mirrored. So click on the Move with Mouse button and reposition the part.htm 2/3/2014 . is to first reposition the part with the mouse and then do some fine-tuning with the parametrical translation and rotation tools. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.Mimics Tutorial Page 65 of 79 As you can see. During repositioning it is also possible to scroll through the axial images to make sure the fit is optimal on all slices. got to the CMF/Simulation menu and choose Reposition. Repositioning To reposition the part. We will reposition this part in the next section of the help. This will open following dialog: Select the Mirrored part and start the repositioning. but not correctly positioned. The easiest way to do this. Keep in mind that you can also reposition in the 2D views so this makes it a lot easier to get a real nice fit. You can translate the part by dragging the center point with your left mouse button and rotate the part by dragging the corners of the selection box with your left mouse button.

Mimics Tutorial Page 66 of 79 When you are happy with the fit. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.htm 2/3/2014 . you can click on the Analyze Motion button to see the final translation and rotation of the part.

The FEA module has to be licensed to be able to follow this tutorial. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. We will start with a dataset of a head and explain how to do the segmentation. you can then export the part and the skull to STL files and continue working on the custom implant in your design software. Browse to the directory where you have installed the extra Tutorial Files and go to the Airway directory. click on the OK button. The topics that will be discussed in this tutorial are:       Importing the images Doing a segmentation Calculating a 3D Object Remeshing the 3D Object Exporting to a Fluent mesh Importing the mesh in Fluent Importing the images In the File menu. CFD Tutorial In the CFD Tutorial we will explain the workflow for creating a 3D model of the throat that is suitable to do a CFD analysis on. select Import Images. how to calculate the 3D and how to remesh the 3D. If you have a license for STL+.Mimics Tutorial Page 67 of 79 To apply the reposition. This tutorial will explain how to link between Mimics and Fluent.htm 2/3/2014 .

so click on the Next button to accept this selection. In the next step you will see the properties of the project. Create a new mask with a lower threshold value of –1024HU and an upper threshold value of –500HU. Doing a segmentation After the import of the images. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.Mimics Tutorial Page 68 of 79 The images in the Airway directory will be selected automatically. Make sure that the skip images setting is 0 and that you use CT as compression method. the images will be imported and a Mimics project will be created in your default working folder.htm 2/3/2014 . By clicking on the Convert button. we can start doing a segmentation of the air in the throat.

choose Edit Mask and choose the erase function. Before manual editing After manual editing Before manual editing After manual editing Next we will isolate the throat from the other parts in the dataset. Then click with the left mouse button on the throat as indicated on the screenshot below.htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. To do this.Mimics Tutorial Page 69 of 79 As you can see.20.80 and remove the green mask from that slice with the manual editing tools.30/25. To do this. then go to the segmentation menu and choose the Region Growing tool. Make sure that your cursor is big enough by pressing the CTRL key and drag the left mouse button.80. this will create a mask that contains all the air in the project.70/55. We will now cut of a part of this segmentation to make sure we only have a small part of the throat. Then go to axial slice 48. Select the Green mask as the source mask and a new mask as the target mask.30/10. go to the segmentation menu. Then do the same for the axial slice 92. go to axial slice 63.

To do this. go to the segmentation menu and select the Calculate 3D Object item. You can now calculate a 3D Object. choose Custom Quality and then click on the Options button.htm 2/3/2014 . This will open the Calculate 3D Parameters dialog where you should use the same settings as below: This will result in following 3D: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Select the Yellow mask from the list.Mimics Tutorial Page 70 of 79 Calculating a 3D Object This will result in a second mask that only contains the throat.

Make sure your interface is looking like the screenshot below and that the triangle visualization mode is selected: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. This will show following dialog: Choose the Yellow 3D Object and click on the OK button. go to the FEA menu and choose Remesh. To do this. We will do this smoothing in the Remesher to make sure that we can contain the sharp edges at the top and bottom of the throat. This will open the Mimics Remesher with the 3D Object loaded.Mimics Tutorial Page 71 of 79 This 3D Object is quite coarse because we are not using any smoothing. Remeshing the 3D Object This 3D Object now has to be remeshed in the Mimics Remesher.htm 2/3/2014 .

first select the in and out surface by selecting the surface selection tool in the mark toolbar and left clicking on the in and out surface: Then select only the mantle by clicking on the Toggle button on the mark toolbar .htm 2/3/2014 . file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Since we don’t want to loose the sharp edges at the in and out surface.Mimics Tutorial Page 72 of 79 Smoothing We will first do a smoothing operation.

do a local smoothing by going to the Tools menu and selecting the Smoothing operation.4 as the maximum quality measure.htm 2/3/2014 . Make sure that the quality parameter is selected in the quality histogram and that you have selected Skewness as quality parameter and Sharp geometry as inspection parameter: Set a value of 0. Make sure that local is selected in the Smoothing dialog: Unmark all triangles by clicking on the Unmark button in the mark toolbar. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. As you can see we have 149 triangles with a quality that is below 0.4. Improve quality Next we will improve the quality of the triangles.Mimics Tutorial Page 73 of 79 Next.

8: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.4.htm 2/3/2014 . We will try to remove these with the Split Based Remeshing operation .Mimics Tutorial Page 74 of 79 Hint: The skewness parameter in the Mimics remesher and the Fluent softwares are inverses. select the Inspection parameter in the Quality histogram and put the Maximum quality threshold to 0.6 in Fluent. So a quality of 0. Sharp Geometry Next we will check for sharp geometries in the part.4=0. To do this. there are no more triangle with a quality below 0.4 in the Mimics Remesher is actually a quality of 1-0. Use following settings and click on OK: Then apply the Split Based Remeshing operation again with following settings: This will result in following 3D Object and quality histogram: As you can see.

Mimics Tutorial Page 75 of 79 Then enable the Group checkmark and the Show All checkmark and set a Boundary level of 2. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. Select the Shell button on the mark toolbar and left click on the in and outlet surfaces. Now. we want to smooth the parts were sharp geometry is occurring. We will refine the mesh where sharp geometry is occurring.5mm. You can do this by calling the Split Based Remeshing algorithm again and by setting a minimum edge length of 0mm and a maximum edge length of 0. again go to the Inspection Parameter and click the Mark Group button. Click on the Mark Group button to select all the triangles that are now on the screen (all triangles that have a sharp geometry that is lower than 0. but we don’t want to change the sharp edges of the in and outlet surfaces. Then.8 + their 2 neighbors).htm 2/3/2014 .

Mimics Tutorial Page 76 of 79 Now select the Smoothing function again.5mm and leave the other settings as before. make sure that the local mode is selected and apply the smoothing: Click on the Unmark button in the mark toolbar again to unmark all triangles. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.htm 2/3/2014 . It is best to select the triangles in this area (with the mark window button ) and do a local split based remeshing with a maximum triangle size of 0. Remove them by using the Split Based Remeshing algorithm again with following settings: Areas with high curvature There are still two areas with high curvature. Go again to the Quality parameter in the quality histogram and you will see that a couple of bad triangles were created during the previous operations.

Make sure that. This sharp angle can be removed if needed during the segmentation or by moving the points causing this sharp angles with the move point tool . Split up in surfaces Mimics will split up your mesh. in the preferences.Mimics Tutorial Page 77 of 79 Areas with sharp edges During our segmentation we have created an in.htm 2/3/2014 . based on the wireframe of your 3D Object. All wireframe that is not closed. the wireframe angle setting is set to 30 degrees: Choose Wire as display mode: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD. So we will first look if the in and outlet surface have a closed wireframe and then if there are other closed wireframes.and outlet surface with a very sharp angle. All surfaces with a closed wireframe will be split up to a separate surface. will be ignored.

both in and outlet surface have a closed wireframe (with the wireframe angle setting on 30 degrees) and they are the only closed wireframes. If you set the wireframe to a higher setting. If you put the wireframe on e. The remesher will ask you if you want to save your changes. you can create and delete wireframe by using the manual remeshing functions and the smoothing function. so we can go back to Mimics by closing the remesher.g. you will notice that the noise wireframe is removed while the wireframe for the in and outlet surfaces still remains. Export to a Fluent mesh The remeshing of the airway is complete. You will see a new 3D Object in Mimics that is called Remeshed_Yellow 1_1.Mimics Tutorial Page 78 of 79 As you can see. so choose Yes. If this would not be the case. This will show following dialog: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.htm 2/3/2014 . but that the wireframe of the in and outlet surface is still closed. You can export this object to a Fluent mesh by going to the Export menu and choosing Fluent. 50 degrees you will see that all noise wireframe is removed.

Import the mesh in Fluent You can then import this fluent file in fluent by using following parameters: file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh1DBD.msh file can then be imported in Gambit or Tgrid and a volume mesh can be created. When you click on the OK button. The resulting . Mimics will ask for a Split Angle. Use the same value of 50 degrees as you have used as wireframe angle in the remesher.Mimics Tutorial Page 79 of 79 Select the Remeshed file and add it to the export list.htm 2/3/2014 .

1 or 7) can be the causes for this problem. If this is not the case. the drive has to be connected correctly. Our drivers operate with the OD and they take care of reading and converting of the data. If you are installing Mimics on an existing computer system. The drivers are installed together with the Mimics software. Frequently Asked Questions Import module 1. It's also important that the user has administrator rights. In order to do this.0 GHz or equivalent 1 GB RAM ATI RADEON or NVIDIA GeForce card with 128 MB RAM Non-interlaced 19" color monitor or 17” flat panel monitor Resolution of 1280x1024 or higher Optical mouse with a scroll wheel Note: To ensure smooth operation of Mimics. the drive is not correctly connected. You can find the latest drivers on the ATI an NVIDIA website.0 Recommended:   Windows 2000 or XP Internet Explorer 6. please refer to the Minimal Specifications to ensure that Mimics will operate on your computer. file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh972. Mimics does not recognize the MOD device. If you intend to purchase a computer for Mimics. We recommend a fast 3D video card that supports OpenGL to speed up the complex 3D calculations used by Mimics. or the SCSI address (0.System Requirements Page 1 of 3 System Requirements Mimics runs under Windows 2000 and XP. in order to access the SCSI devices. make sure to update your graphic card drivers. The monitor should be a high quality. non-interlaced color monitor to ensure sharp and accurate images. the dipswitch settings. we strongly urge you to use the Recommended Specifications as a guide. It operates on any Pentium class personal computer as long as the video memory is at least 4MB so that it supports a 1024x768 resolution with 24 bit colors.0 Hardware Requirements: Minimal:     Intel Pentium II 300 MHz or equivalent 256 MB RAM Graphics card supporting 1024x768 and 16-bit color with 4 MB RAM Non-interlaced 15" color monitor Recommended:       Intel Pentium 4 3. A bad wire. The following questions help to detect the problem: When you start the PC. do you see the drive displayed in the list? This is important to know whether the PC recognizes the drive.htm 2/3/2014 . Software Requirements: Minimal:   Windows 2000 Internet Explorer 5. a terminator problem.

Mimics can read all images that are parallel. It could be that only users with administrator rights have the permission to write to certain folders. I can’t find the file in the target folder. 2. No problem with big file sizes. Make sure you have the permission to write to the target folder.65000. This info should be stored in a txt file that has to load via the "Import table positions from" function in the Manual conversion window. If this file can't be found. once they are converted. Mimics also provide a loss less compression. 8. It is unreconstructed. Check if the disk is not empty. most of these gray values will be put on -1024 HU and this may cause images without contrast. This CT compression is useful in datasets with a wider range of gray shades. so that this problem doesn't occur anymore. You can simply read the table position on the axial view in Mimics. Since the scan site is customer. then you must know that only 1 data block can be read from this MOD. You should use the direct interface: in the RP Slice module you can calculate SLC files that can be loaded in the Lightyear software. you can create a dataset based on these images. the situation is a bit more complicated but not impossible. like a tape drive. set per set. Are data sets with varying slice distances supported? If the file format is supported. see our troubleshooting page in the help files (via General. When I import images from an MOD. 5. Start testing the SCSI devices. In the Manual import dialog you see at the right bottom corner "Maximum Image Value". restart Mimics and try to import again. try without any of these other drives connected. all gray values are scaled/translated to the range of 0 . This comes from our medical background and also allows more compression on the data (12 bit data). If you don't see the drive in the list. the message "Cannot process DICOMDIR" is shown and nothing is read. When a manual import is needed (because the file format is not known). The table position is read from the header of the file and used afterwards in the Mimics. so varying distances are supported. When trying to import DICOM images. I get no-contrast images in Mimics. It's probably a DOS formatted disk with DICOM images that is being read. When I export an STL file. the images look fine. 12. How to read images from Unix formatted disks? Unix formatted disks can be read like other optical disks in Mimics 7. not the volume data/RAW data without header. If this value is a lower than the real maximum value in the dataset. Also check if the option "hide file extensions for known types" is unchecked in Windows Explorer > View Menu > Folder Options. it can be implemented/supported if we get the help of the customer. The images need to be uncompressed. If the scanner and/or file format is unknown. but it will not be possible to generate a nice 3D model. The model will look less stair-stepped..2 and later versions. you can pile up all images again at the correct position. where it will filter out the noise in the air..htm 2/3/2014 . This method has 3 advantages: 1. A TAC Helicoidal Marconi Twin is an example of a scanner that writes UNIX formatted disks. they have to put each patient data on a different Picker MOD. Once the SLC file is loaded in Lightyear. so also which image is on which table position. my patient is not listed. even though the preview window looked good. Mimics tries to contact the connected SCSI devices. while the interval should be 0. When I convert Tiff images I got no-contrast images. 2. the first 200 gray values in the data set will be changed to the Hounsfield unit -1024. the maximum pixel value is 4096. each of these sets can be imported. If it's a Picker MOD. In the dialog box that appears. disable the Ënable SCSI”checkbox. CT compression is a lossy compression.4095. You will need to know all parameters upfront. Trouble Shooting). 14. When using loss less compression. have the same size and contain gray values. Input of Mimics The Raw data is the data as it comes off the scanner in Fourier space. The reason why it causes problems is that one (or more) of these devices give error messages. 4. my computer reboots. Click OK. a ZIP drive? If yes. because it is already sliced. Having this information makes it easier for us to implement this. 10. Open Mimics and select from the file menu: Options --> Advanced SCSI. then Mimics can't import the images and gives you this warning. But you have to make sure that you adjust the "first table position" parameter for every set. First check both sides of the optical disk. it's no problem for Mimics to read them. This means that only 1 patient can be read at a time. In mimics there is a function to block the messages from certain devices. start Mimics and choose "Advanced SCSI" in the Options menu. you just have to click "prepare". Cubical interpolation can be applied.System Requirements Page 2 of 3 Are there other devices connected to the PC. When you know this. STL+ 13. When you select CT compression during conversion. because it's very strange for the DICOMDIR to be missing. When importing data in Mimics. You can make the combination again of all sets with the "organize images" function. it is easier for them to obtain the information about disk formatting and file formatting from the scanner manufacturer.. The reconstructed images slices are input for Mimics. In order to read all patient data.. High resolution can be kept. If the SCSI device is listed during start-up. Make also sure that there is enough space on the hard disk. If you have a dataset with a narrow gray value range. The size of the STL file becomes so high that it's very difficult to handle in LightYear software. CT-Convert. If the images are binary. 3. 9. Each time I select Import images from the File menu. When I import images. If there are groups of images with the same size (= sets of succeeding images). the images are automatically read and converted. Also calculate the support file with RP Slice! MEDCAD General file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh972. On these disks there's normally a file called DICOMDIR that lists all the images on disk. When importing images. When I import images and use CT compression. 7. 6. it may cause images without contrast. Like this.

then written to the same optical disk as the previous scan. open them one by one in Mimics and look in the project information dialog box to see the study date and time (if this is available in the header file). Contact Info Europe (Headquarters) Materialise Technologielaan 15 3001 Leuven Phone +32 16 39 66 11 mimics@materialise.htm 2/3/2014 . S25 2JZ Phone +44 1 909 552 300 software@materialise-rp. If a patient is rescanned. 2) Click on an image in the preview window on the right to leave it out of the project.com United Kingdom Unit 1. Suite 200 Ann Arbor. MI 48103 Phone +1 888 662-5057 mimics@materialise. GunPoity..com. in other words. South Phone: +82 31 479 7320 software@materialise.my Japan Materialise Japan K. click again on the image. All selected images will be left out of the project. Brooklands Way Brooklands Park Ind. 20.2 mm). Typically such errors are caused by a defect memory or a corrupt disk. hardware problems. The projects are not listed in a chronological order.cn Malaysia Materialise Unit D6-03 Phileo Damansara 1 No 9 Jln. Yokohama Phone +81 45 440 4591 software@materialise. PRC Postal Code: 200122 Phone + 8621 58312406 software@materialise.com. How to organize images. To leave out some of the images you can proceed in two ways: 1) In the list on the left. Avenue de la Déportation 26100 Romans-sur-Iscre Phone +33 4 75 05 00 22 software@materialise. What are the deviations between the dimensions of a reconstructed model of a reference or calibration body compared to its real dimensions? Because our interpolation algorithms are designed to be able to use sub pixel values. 18.co.co.K Yokohama Portside Bldg. 2F Sakae-cho 8-1 Kanagawa-ku.fr China Room 1606. I had a few times a blue screen while working with Mimics.be USA & Canada Materialise 6111 Jackson Rd. Bao An Mansion No. In the Open project dialog box. Rotherham.co. 0. Dinnington. 800 Dong Fang Road. the 3D reconstruction calculation has a maximal error of 1/2 pixel size (mostly at max.de France Zone Industrielle 41.uk Germany Landsberger Strasse 476 D-81241 München Phone +49 89 88 94 96 30 software@materialise. how can you tell which is the old scan and which is the new scan? You can't tell from the import images dialog box what scan is the old one or the new scan. 19. KyungKi-Do. you can't find it out either. If you want it back into the project. The only way to distinguish between them in this situation is to convert them both. you can select all images you want to leave out the project and then click on the V-sign of a line.jp Korea #912. HanLim Human Tower. Open the project in Mimics and go to File --> Organize images. Pudong Shangai. Or you can use the Add and Remove buttons on the bottom of the window.System Requirements Page 3 of 3 16. 16/11 46350 Petaling Jaya Phone +60 3 76652988 software@materialise. 435-824. All images with a V-sign will be used in the project. GeumJeong-Dong.kr file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh972. Est. 1-40.