User Guide to The Computational Morphometry Toolkit1

Release 1.10

Torsten Rohlfing
August 6, 2010 Neuroscience Program, SRI International, Menlo Park, CA2
Abstract This guide is intended as a very brief introduction of the main tools in the Computational Morphometry Toolkit (CMTK), which is available in source code and as pre-compiled binaries from http://www.nitrc.org/projects/cmtk/. The target audience of this document are CMTK users, who might use this document as a reference to the most common processing tasks, and prospective users, who may find this information useful to determine whether CMTK provides functionality that they can use. We focus in particular on a simplified workflow for deformation morphometry studies based on magnetic resonance images: DICOM conversion, artifact correction, affine and nonlinear image registration, reformatting, Jacobian determinant map generation, and statistical hypothesis testing.

1 This

2 Continued

document is licensed under the Creative Commons Attribution License Version 3.0. development and maintenance of CMTK is funded by the NIBIB under Grant No. R01 EB008381.

Contents

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Contents
1 Introduction 1.1 Coordinate Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Registration Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Supported Image File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Step-by-Step Morphometry 2.1 DICOM Image Stacker . . . . . . . . . . . . 2.2 Interleaved Image Motion Artifact Correction 2.3 MR Intensity Bias Field Correction . . . . . . 2.4 Affine Image Registration . . . . . . . . . . . 2.5 Nonrigid Image Registration . . . . . . . . . 2.6 Reformating Registered Images . . . . . . . 2.7 Jacobian Determinant Maps . . . . . . . . . 2.8 Statistical Testing . . . . . . . . . . . . . . . 2.9 Atlas-based Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3 3 4 6 6 7 7 7 9 10 10 11 11

3 Atlas Construction 15 3.1 Averaging Pairwise Correspondences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 3.2 Iterative Shape Averaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 3.3 Groupwise Population Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 4 More Gory Details 16 4.1 Registration Options for Image Pre-Processing . . . . . . . . . . . . . . . . . . . . . . . . 16 4.2 GPU-Accelerated Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Index 20

Consequently. By definition. which we refer to as “RAS” coordinates.” the y direction increases towards the anatomical “Anterior. can be checked out from the CMTK Subversion repository via svn co https://nitrc.nokia. CMTK is primarily a collection of command line tools. This means that the storage order of image pixels in memory is such that the fastest-varying of the three pixel indexes corresponds to the “Left”–”Right” anatomical direction. All images that are read into one of CMTK’s tools are first reoriented to fit this coordinate system.” and the z direction increases towards the anatomical “Superior.0 or higher). can be used as a relatively lightweight. thus coincides with the “Left-Posterior-Inferior” corner of the image volume.1 Coordinate Conventions For medical image data. CMTK determines the nearest anatomical orientation of the image within ±45 degrees around each rotation axis.2 Registration Terminology Since one of the primary strengths of CMTK is its selection of powerful and well-tested registration tools. the first pixel in memory is the one that is the Left-Posterior-Inferior-most pixel anatomically. including all figures. respectively.com .3. yet powerful. the second fastest to the “Posterior”– ”Anterior” direction. CMTK’s back-end libraries. 1. adequately named “triplanar . CMTK is available both in source code (licensed under the GNU GPL3) and as pre-compiled binaries from http://www. throughout this guide as well as in all tools and source code. is a set of software tools that perform various types of processing and analysis on three-dimensional (3D) image data. CMTK comes with a very simple triplanar image viewer (see screen shot in Fig. and the “BUILD_GUI ” build option must be enabled.nitrc. For image file formats that define subject orientation based on direction vectors within an anatomy-based coordinate space.” The coordinates shown in this viewer for any image are exactly the coordinates that all CMTK tools use. we shall refer to one image as the reference and the other as the floating image. (0. or short CMTK. 1). This means that the x direction of the coordinate space increases towards the anatomical “Right. 0). A LTEX source for this User Guide. which is the majority of modern formats.” The coordinate space origin.3 1 Introduction The Computational Morphometry Toolkit. CMTK uses an anatomy-based coordinate system. and to diagnose problems. In pairwise registration. platform for implementation of new image processing algorithms. Others may refer to these as the fixed and the moving image. we shall first clarify some important registration terminology. In addition. all coordinate transformations computed by CMTK are functions that map from the space of the reference 1 http://qt. which make the toolkit ideally suited for unattended batch processing of large amounts of data. CMTK must be built with support for the Qt toolkit1 (version 4. Note that for the triplanar viewer to be available.org/svn/cmtk/trunk/doc/UserGuideCMTK/ 1. which are shared by all command line tools.org/ projects/cmtk/ . To confirm that images are read correctly. and the slowest varying to the “Inferior”–”Superior” direction. 0.

hdr and example. The following suffixes are supported: nii Single-file NIfTI-1 image3 .net/nrrd/ . both for import and export.nimh.sourceforge. it is the floating image by default that will be transformed to match the reference image. Whether a particular file can be read into CMTK can easily be tested using CMTK’s describe tool. 2 http://eeg.hdr When writing files.hdr nrrd Single-file Nrrd4 . Note that in order to correctly identify the format of images with separate header and data files. such as landmarks or the nodes in a mesh. its type is detected automatically.3 Supported Image File Formats CMTK supports a wide range of image file formats.pdf 3 http://nifti. For example. to test (and describe) the content of an Analyze 7.img . not the data file.gov/nifti-1/ 4 http://teem. example. when reformatting one image to match the other.net/ANALYZE75. img NIfTI image with detached header.nih. (fixed) image to the space of the floating (moving) image. CMTK determines the desired file format based on the suffix of the output path.1. then the coordinates of the reference image will be transformed to match the floating image.52 header/image pair. it is necessary to provide CMTK with the path to the header file. 1. Note that when we speak about transforming coordinates of features.sourceforge. one would run the following command: describe example. When reading an image file into CMTK. Header file will be written with suffix . As a result.3 Supported Image File Formats 4 Figure 1: Screen shot of CMTK’s triplanar image viewer.

hdr and . whereas the . The data file will be written with suffix img . For historic reasons. Because CMTK contains a bundled zlib library. Note also that. all data files are written with gzip compression. Thus. Both formats need to be read using the . Note that both Analyze and NIfTI header/data file pairs use the suffixes . by default. this is true even when the gzip tool itself is not installed. hdr Analyze 7. to re-enable compressed writing.hdr as the output file suffix will always invoke Analyze export.img .1.img suffix will invoke NIfTI export.hdr file. On a Unix/Linux system using disabled by defining the CMTK_WRITE_UNCOMPRESSED the csh shell. use unset CMTK_WRITE_UNCOMPRESSED or its appropriate equivalent inside your favorite shell. The data file will be written with . however.5 detached header. rather than setting the variable to “0” for example. and its value is ignored.3 Supported Image File Formats 5 nhdr Nrrd with detached header.raw suffix. . this would be achieved via export CMTK_WRITE_UNCOMPRESSED=1 where only the definition of the variable is relevant. This behavior can be environment variable. using .

nii /path/to/dicom or short dcm2image -r -O image%N. image-2. For example. the command dcm2image --recurse --out-pattern image%N. Note that a complete list of supported options can always be obtained by running a given tool with the --help command line option. CMTK provides a tool that can search through a file system tree.nii . image-1. It is not intended to provide a complete list of available tools.1 DICOM Image Stacker When dealing with 3D medical image data in particular. 2 Step-by-Step Morphometry This section provides a step-by-step guide to the tools used in a typical morphometry study using the CMTK tools. find all DICOM files in it. . 2. To this end. the first step of processing is usually the conversion of a stack of single-slice image files in DICOM format to a single-file 3D image. and so on.6 Figure 2: Example of interleaved image before (left) and after (right) correction of motion artifacts using the film tool. group the ones that form 3D image volumes. We are also not covering all available options of each tool.nii . These are roughly mid-sagittal slices through a late-echo FSE image acquired in three interleaved passes. and write each of these volumes into a separate file in one of the supported formats.nii /path/to/dicom would recursively search the file system under /path/to/dicom and write all resulting image volumes to consecutively numbered image files in NIfTI format.

nii spgr.2. the tool can generate its own mask via the --thresh-min and --thresh-max command line parameters. The mrbias tool. 2 for an example). such as abdominal images.nii image. the tool writes an image that is the resulting level set function. More technical detail about our implementation in particular can be found in Ref. and all passes are co-registered using rigid intensity-based registration to determine the inter-pass motion parameters. Computation is constrained via a (binary) mask that is read from the foreground. 3).nii foreground. [18]. CMTK implements an algorithm for post-reconstruction correction of these artifacts [22] in the film tool (for “Fix InterLeaved Motion”). implements an algorithm similar to the multi-resolution algorithm by Studholme et al. the film tool needs to be given the number of passes in the interleaved images. albeit only in German. for example for a three-pass image: film --passes 3 input. the tool implements an extreme simplification of the algorithm for segmentation without edges by Chan & Vese [5]. CMTK provides a very simple “level set-type” segmentation tool: levelset --binarize spgr.nii In most cases.nii In very broad terms. works well on human as well as non-human images (Fig. the interleaved image stack is separated into the original passes. Second. subject motion between the passes can lead to characteristic artifacts in the final. The film tool operates in three stages: first. By default. which is then refined in the third stage using an iterative inverse interpolation algorithm (see Ref. One of the advantages of this particular algorithm for intensity bias field correction is that it does not involve a model of either the anatomy in the image or the tissue types that are present. and on brain as well as non-brain anatomy. interleaved image stack (see Fig. therefore. but using the --binarize switch turns the output into a thresholded.nii spgr_corrected. registration . is typically called as follows: mrbias --degree-mul 2 --mask foreground. [28].3 MR Intensity Bias Field Correction CMTK implements a model-free algorithm for intensity bias field correction based on minimization of image entropy [13].nii corrected. binary mask that is appropriate for use by the mrbias tool. Alternatively. 2. motion-corrected image. 2.2 Interleaved Image Motion Artifact Correction When MR images are acquired as multiple interleaved sparse image stacks (“passes”). It. [22] for details). volume injection is used to obtain a coarse reconstructed.2 Interleaved Image Motion Artifact Correction 7 2. For proper operation. To generate foreground masks automatically. the through-plane acquisition direction can be guessed from the data.nii which computes a second-order polynomial multiplicative bias field.4 Affine Image Registration The basic pairwise image registration tool in CMTK. . which implements this algorithm.

Top row: applied to a human brain SPGR image acquired at 3T. Bottom row: applied to a rat brain early-echo FSE image acquired at 3T.2.4 Affine Image Registration 8 Original Corrected Figure 3: Examples of MR intensity bias field correction using a second-order polynomial multiplicative bias field computed by the mrbias tool. .

nii flt. translation and rotation of a 3D rigid transformation. i.xform ref. 9 DOFs are optimized.xform registration --initial initial.xform --grid-spacing 40 --initial affine. however..xform ref. Afterwards. [25]. anisotropic scale).g. 31] (--mi ). which uses as its transformation model multi-resolution free-form deformations based on cubic spline interpolation between sparse.xform can be run as follows: warp -o ffd40. the make_initial_affine tool can be used. and shears).nii . rotation). and constrain the deformation using grid bending energy: warp -o ffd5.xform --dofs 6.nii Typically. [21].xform --grid-spacing 40 --refine 3 --energy-weight 1e-1 \ --initial affine.9 --auto-multi-level 4 \ -o affine.5 Nonrigid Image Registration 9 In order to compute an affine registration between two images. principal axes [1]. and image orientation vectors (e. 7 (similarity: translation. and correlation ratio [17] (--cr ) In the above example. was described in Ref.nii 2. A very simple nonrigid registration using a 40 mm control point grid. Our particular implementation.2. 3 (translation only).nii initial. mean squared difference (--msd ). scale. for testing).9 --auto-multi-level 4 \ -o affine. to the reference image. rotation. the registration transformation is initialized (via --initxlate ) by translating the floating image’s center to that of the reference image. where all optimization and image resampling parameters are automatically determined for a 4-level multi-resolution procedure. registering floating image flt.nii This performs a registration of the floating image. registration uses the normalized mutual information [29] image similarity measure. rotation. in order to first initialize a transformation using principal axes and then use the result as the initial transformation for intensity-based refinement. i. Other available similarity measures are: standard mutual information [14. At each resolution level.5 Nonrigid Image Registration Pairwise nonrigid image registration in CMTK implements an algorithm introduced by Rueckert et al..nii to reference image ref. By default.nii . one would want to run a more sophisticated multi-level deformation. and 12 (full affine: translation. which supports centers of mass. rotation.xform ref.nii flt. as provided by the original DICOM data). three anisotropic scale factors in addition to the translational and rotational parameters.nii . flt. normalized cross-correlation (--ncc ).. the registration first optimizes 6 degrees of freedom (DOF). global scale).nii flt. which uses SMP parallelism to take advantage of multi-CPU systems.nii flt. the registration tool can be run as follows: registration --initxlate --dofs 6. uniformly distributed control points.e. ref.nii based on an affine transformation affine.e.xform ref. For more complex initializations. Supported DOF numbers are: 0 (no registration.nii flt. 6 (rigid: translation. For example. say with three refinements (each reducing the grid spacing by 1/2 for a final spacing of 5 mm). 9 (translation. one would use the following sequence of commands: make_initial_xform --principal-axes ref.

In the simplest case.nii flt.xform More interestingly.6 Reformating Registered Images To reformat the registered floating image following the examples in the previous section. such as reformatx -o reformat. reformatx uses trilinear interpolation. The command to compute the appropriate Jacobian determinant map.nii and time1.xform between two images.nii \ img1. For the resulting location. we can compute the Jacobian analytically at any location in the domain of . it is possible to instead constrain the Jacobian determinant of the deformation to be nonzero.xform ref.nii atlas. Then.xform The somewhat unintuitive order of arguments on the command line is due to the versatility of the reformatx tool.xform --jacobian time1_to_time2. can also be computed using the reformatx tool. is then computed.xform --inverse img3_to_2.nii ffd5.6 Reformating Registered Images 10 To prevent folding of the deformation grid. say we want to compare these Jacobian maps from multiple subjects.7 Jacobian Determinant Maps Jacobian determinant maps.xform --grid-spacing 40 --refine 3 --jacobian-weight 1e-5 \ --initial affine.xform . run reformatx -o reformat.nii img1_to_2.nii .nii 2. is then reformatx -o jacobian. which are a staple ingredient of deformation-based morphometry studies [2].xform .2. jacobian. every sample coordinate in atlas space is first mapped to subject time 1 space via atlas_to_time1. say images time1. Because the nonrigid transformations computed by the warp tool are generated via continuously differentiable B-spline basis functions. time1_to_time2. we may want to compute the Jacobian determinant map for a transformation time1_to_time2. the Jacobian determinant of the longitudinal transformation. but it also supports cubic (--cubic ) and cosinewindowed sinc (--sinc-cosine ) interpolation for intensity images. all in the space of a common atlas coordinate system. we can directly compute the maps in atlas space by concatenation of transformations: reformatx -o jacobian.nii acquired from the same subject at two time points.nii ref. partial volume interpolation [14] (--pv ) for label images.xform Here.nii --floating img3. instead of computing each map first in each subject’s coordinate system and then reformatting these maps into atlas space. 2.xform By default.nii time1.nii --floating flt. and nearest neighbor (--nn ) interpolation for all types of images. which is achieved by changing the above command as follows: warp -o ffd5.nii \ atlas_to_time1. which allows for the concatenation of arbitrary transformations (and their inverses).nii --jacobian time1_to_time2.

and atlas_labels.jacobianB1.nii jacobianA2. atlas_image. 24].nii jacobianA1. make sure that there are an equal number of images before and after the “-.” anywhere in the image list).nii --tstats-file tstats.nii .nii \ jacobianA1. that is.nii --tstats-file tstats.nii jacobianB2. for example an MR scan of a new subject. tissue probability maps.nii atlas_image. and any transformation can additionally be inverted by prefixing it with --inverse (affine transformations are inverted explicitly. The standard atlas of CMTK is the SRI24 atlas [23.nii is a new.9 Atlas-based Segmentation Atlas-based segmentation uses correspondence between a previously segmented image (the atlas) and a new. reformat that atlas label map onto it. CMTK also provides an integrated atlas-based segmentation tool. For convenience. 2.nii .nii -. To compute a two-tailed paired t-test. the segmentation corresponding to the atlas intensity image. The tool will then register the atlas to the new image. and the t-statistics are also written to tstats.jacobianB1. however. for example.nii atlas_labels..nii This computes a pixel-wise two-tailed unpaired t-test between the two lists of images separated with “-. and write the result to the file output_labels.nii is the intensity image of the atlas. The resulting p-values image is then written to pvalues. whereas nonrigid transformations are inverted numerically). In the simplest case.nii is the label image of the atlas.” on the command line. the ttest tool computes different types of t-tests (all two-tailed) and statistics. two populations A and B of maps can be tested against one another as follows: ttest -o pvalues.nii jacobianA2. warp .nii 2. unsegmented image to create a segmentation of the latter [16]. Jacobian determinant maps between different subject groups.nii --paired \ jacobianA1. it is assumed that input_image. i. and segmentation .8 Statistical Testing For group comparisons of. will compute a single-sample t-test.nii jacobianB2.nii Invoking ttest with only a single group of images (without “-.nii Here. which can be run as follows: asegment input_image. as well as scalar diffusion measures. This relatively simple idea can easily be implemented using CMTK’s registration .nii -. a test for significant differences from zero: ttest -o pvalues. Note that the reformatx tool allows an arbitrary number of transformations to be listed both before and after the --jacobian switch.e.8 Statistical Testing 11 the transformation.2.” separator and that corresponding images in both groups are in the same order. unsegmented image. then add the --paired option and run ttest -o pvalues.nii jacobianA2. which means that the direct computation of Jacobians into atlas space does indeed avoid one interpolation of the Jacobian determinant map.nii output_labels. which comprises several different channels of MR image information.nii .nii --tstats-file tstats. and reformatx tools.

It then creates and writes a segmentation map based on the “tzo116plus” label map. which uses the SRI24 atlas is also built. “lpba40 ” for a segmentation based on the 40-subject LONI Probabilistic Brain Atlas [27] (LPBA40).2. This tool.org . GM) segmentation. and “tissue ” for a maximum-likelihood threetissue (CSF. which is the default. as well as the result of an atlas-based segmentation using the “tzo116plus ” label map.“early-fse ” for early-echo (proton density-weighted) FSE . Likewise. WM. This is achieved simply by running asegment_sri24 input_image. asegment_sri24 .nii output_segmentation. registers a given image to the SPGR channel of the SRI24 atlas. selected using the --registration-channel mand line option: “spgr ” for T1-weighted SPGR. [30]. by default. then a simplified segmentation tool. “late-fse ” for late-echo (T2-weighted) FSE. The integration of a complete atlas-based segmentation workflow with a pre-defined atlas is particularly convenient when using CMTK’s tools from within the 3D Slicer5 .slicer. 5 http://www. different label maps are available for the output.9 Atlas-based Segmentation 12 maps. 5 shows an example of the Slicergenerated user interface for the asegment_sri24 tool. If CMTK is configured and built with SRI24 support (by setting the CMTK_ROOT_PATH_SRI24 CMake variable). and “fa ” for DTI-derived fractional anisotropy. which derived from the “automatic anatomic labelling” (AAL) parcellation map by Tzourio-Mazoyer et al. selected by the --label-map command line option: “tzo116plus ” for the extended Tzourio-Mazoyer map. Fig.nii comDifferent atlas channels can be used for registration.

] a . Universit¨ t Marburg (Germany). Both examples were computed by running the levelset tool with default settings and no image-specific parameters. Bottom row: fluorescent confocal laser scanning microscopy image of a locust brain [10]. [Locust images courtesy of U.2. Homberg.9 Atlas-based Segmentation 13 Image Mask Image with Mask Outline Figure 4: Examples of foreground/background segmentation using the levelset tool. Top row: SPGR image acquired at 3T.

and result of segmentation using the . sri24 tool into 3D Slicer.2.9 Atlas-based Segmentation 14 Figure 5: Integration of asegment “tzo116plus ” label map.

3.nii img1.nii xform03 img0. CMTK implements a groupwise registration algorithm called “congealing” [12]. one of which has been selected as the initial reference image. among other applications.nii img2. congeal and congeal warp were used.nii 3.nii xform02 img0.2 Iterative Shape Averaging The iterative shape averaging (ISA) procedure [20] was first used to create a standard atlas of the honeybee brain [4].nii img4.sh .1 Averaging Pairwise Correspondences Based on pairwise registrations between images in a group and a single selected reference image. its tools have been used to create several published brain atlases of humans and different insect species. Indeed. 24].3 Groupwise Population Registration Direct groupwise registration avoids the need to select an image as the (initial or final) reference and is. this script can be called as follows: sh iterative_shape_averaging. To average three images. and has since been applied to other insect species as well [10. called avg adm .nii -o atlas. 7].nii xform01 xform02 xform03 xform04 CMTK’s tools have been used in this way to create a registration template for a study of the olfactory system of the fruit fly [9]. to create the publicly available SRI24 atlas of normal human brain anatomy [23. CMTK provides a shell script. iterative shape averaging.nii flt_image1. an atlas can be created as the average intensity image deformed by the inverse average deformation [8]. that largely automates the iterative averaging process. [6. then apply avg adm to compute the actual average: warp -o warp -o warp -o warp -o avg_adm xform01 img0.nii xform04 img0. A typical processing sequence using this tool for averaging five images would first compute (using warp ) the nonrigid transformations from a selected reference to the other images. computing the average deformation field is related to the concept of the Active Deformation Model (ADM) introduced by Frangi et al. considered unbiased with respect to such choice. therefore. 11]. CMTK also provides tools that can be used in the construction of atlases. 3.15 3 Atlas Construction In addition to being useful for atlas-based segmentation. As CMTK’s warp tool computes nonrigid transformations based on the B-spline free-form deformation model. somewhat consequently.sh ref_image.nii flt_image2. The tool to compute the average image in average coordinates is. . both using the affine and the B-spline FFD transformation models [3]. The two command line tools.nii img3.

16 4 More Gory Details 4. registration and warp . This is quite effective to prevent degeneration of histograms by extreme image intensities due to noise. and the numbers of histogram bin are set to the number of labels in each image rather than being adjusted based on the intensity range and number of pixels. • Cropping: Images can be cropped. this operation truncates the intensity range of the image such that both the lowest and the highest histogram bin receive 1/NumberOfBins of the total number of image samples. but OpenCL may be supported in future releases. This can be “grey. CMTK is adding support for accelerating computations using generalpurpose graphics processing units (GPGPU).” or “label. When the data class is set to “label. the intensities of the floating image can be Histogram Matching: Using the --match-histograms rescaled to match the distribution of the reference image. Cropping can also improve registration accuracy and robustness by excluding non-informative areas of the images. registration of inter-subject images using the mean squared differences metric.2 GPU-Accelerated Tools Starting with the 1. The command line tools that provide CUDA support are distinguished from their CPU-only counterparts by the suffix “ cuda ” such that the GPU-analog for the mrbias tool would be mrbias cuda .” Typically. The most commonly used of these are: • Data Class: For each image. This is a common pre-processing operator to allow. As of release 1. but the CPU tools could still be used on a system without these capabilities. MR bias field correction. We chose to separate CPU and GPU tools so that both could be built jointly on a system with GPU hardware and drivers. . GPU support is available for level set segmentation.” “binary. which may help increase registration robustness.” the registration algorithm uses nearest neighbour instead of trilinear interpolation.2. support a number of preprocessing operations that can be applied to the reference and floating image on-the-fly. • Thresholding: Upper and lower thresholds can be defined to truncate the image intensities. GPU support is limited to the nVidia CUDA programming model. 4. based on either image index ranges or image coordinate ranges.1 Registration Options for Image Pre-Processing Both the affine and nonrigid pairwise image registration. This artificially increases the overlapping image region that can be considered for registration. and image symmetry plane computation. prior to registration. The registration tool implements a volume clipping algorithm [19] that considerably speeds up registration of cropped images. this is not always fully possible. Setting value outside FOV: A default value for data outside the floating image FOV can be defined using the --force-outside-value option. • Histogram Pruning: For a given number of histogram bins (128 is typically a good value). option. for example.4 release series. the “class” of the image data can be defined. both images should have data in the same class. Note that while every effort is made to keep the command line syntax and semantics identical for CPU and GPU tools.4. . For the time being.

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7 reformatx . 11 registration constraint. 16 Coordinate system. 16 CUDA. 3 Segmentation atlas-based. 16 Image fixed. 15 LPBA40. 7. 16 Slicer software. 12 . 10 registration .Index Artifacts intensity bias field. 9 mrbias . 9 terminology. 10 Registration affine. 3 Jacobian determinant maps. 3. 7 motion. 11 avg adm . 10. 7 principal axes. 11. 11 level set. 3 reference. 6 GPU. 15. 9 DICOM. 16 OpenCL. 3 degrees of freedom. 7 moving. 15 nonrigid. 3 floating. 3 CMTK Tools asegment . 11 warp . 15 CMTK licensing. 9 groupwise. 12 SRI24. 9. 7 make initial affine . 15 congeal warp . 15 dcm2image . 7 Atlas AAL template. 3 interleaved MR. 7. 9 pairwise. 15 congeal . 6 film . 16 ttest . 12 construction.

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