syngo MR B15V

Operator Manual – Spectroscopy

www.siemens.com/medical
This product bears a CE marking in accordance
with the provisions of council directive 93/42/
EEC of June 14th, 1993 for medical devices.
The CE marking applies only to medico-techni-
cal products/medical products introduced in
connection with the above-mentioned com-
prehensive EC directives.
System Information

System type:

Serial number:

Gradient
configuration:

Connected
cameras:

Software options:

Customer service
phone numbers:

3
Table of Contents

Introduction .......................................8
Layout of Operator Manual: ................. 8
Configuration ...................................... 9
Intended use ..................................... 10

Basics...............................................12
Focus in MR spectroscopy (MRS) ........ 12
Localization techniques...................... 12
Spectra and anatomical position ........ 13

Measurement...................................14
Overview of spectroscopy
measurements................................... 14
Positioning patient and coils .............. 16
Generating the measurement
program ............................................ 17
MRS with scan@center....................... 18
Planning in non-isocentric reference
images .............................................. 19
Planning in isocentric reference
images ............................................. 20
Measure scan@center reference
images ............................................. 21
CSI: Transfer slice positioning............. 22
Positioning the CSI slice ..................... 23
CSI: Suppressing interference
signals............................................... 24
Optional: Starting protocol
adjustments ...................................... 25
Optional: Shimming interactively ....... 26
Optional: Improving shim results ....... 27
Optional: Adjusting the frequency...... 29
Measuring raw data ........................... 30

Evaluation ........................................32
Overview of syngo spectroscopy
evaluations........................................ 32
Displaying spectra (example: CSI)....... 33
Select another CSI slice
(example: 3D-CSI).............................. 34

4
 Look for a suitable reference
image ................................................ 36
CSI: Hiding graphics in reference
images............................................... 37
Scaling the display ............................. 38
Showing peak information ................. 39
Performing phase correction .............. 41
Adding a peak .................................... 42
Saving the post-processing
protocol ............................................. 44
Evaluating raw data with a
different post-processing protocol ...... 45
Creating a spectral map...................... 46
Generating metabolite images ........... 48
Showing a metabolite movie .............. 50
Calculating the sum spectrum ............ 51
Generating a result table .................... 52
Saving results..................................... 53
Filming and printing them.................. 54
Examples of spectra 1H MRS ............... 56

Breast .............................................. 58
1H MRS SVS for the breast .................. 58
Positioning the patient and
the coil .............................................. 58
Performing external reference
measurements ................................... 60
Planning the VOI ............................... 60
Suppressing interference signals ........ 61
Normalizing the choline signal ........... 63
Examples of spectra ........................... 64

Prostate ........................................... 66
1
H MRS CSI for the prostate ............... 66
Positioning the patient and coil .......... 67
Planning the VOI ................................ 67
Measurement .................................... 67
Suppressing fat signals ....................... 67
Examples of spectra ........................... 68

5
Table of Contents

Multi-nucleus ...................................70
Multinuclear spectroscopy ................. 70
31
P MRS of the muscle, heart
or liver (31P head protocols for
3 Tesla only) ...................................... 70
Positioning the patient and coil .......... 71
Planning the VOI................................ 72
Setting the measurement
parameters ........................................ 72
Multinuclear frequency
adjustment ........................................ 73
Multinuclear transmitter
adjustment ........................................ 74
Examples of spectra ........................... 75

Protocol management ......................76

Creating a new protocol directory....... 76
Importing customer protocols ............ 77
Exporting customer protocols ............ 78
Delete customer protocols ................. 79

Exporting raw data ...........................80

Exporting raw data in
DICOM format ................................... 80
Exporting raw data as an
ASCII file ........................................... 81

6
7
Introduction

To operate the MR system accurately and

safely, the operating personnel have to have
the necessary expertise as well as knowledge
of the entire operator manual. It has to be read
carefully prior to starting up the MR system.

Layout of Operator Manual:

To improve readability, your complete operator
manual has been broken down into several
individual operator manuals with thematically
distinct content:
❏ Hardware components
(system, coils, etc.)
❏ Software (measurement, evaluation, etc.)
Information for the operator of the MR system
is another part of the complete operator man-
ual.
The volume of smaller operator manuals that
you receive depends on your system configu-
ration, and may vary.
All parts of the complete operator manual may
contain safety information requiring strict
adherence.
The operator manual for hardware and soft-
ware are intended for authorized users. They
assume a basic knowledge of working with PCs
and software.

8
This manual includes descriptions covering
standard as well as optional software Consult
the respective Siemens sales organization to
determine the type of software available for
your system. The description of an option is
not legally binding for providing this option.
The graphics, figures, and medical images
used in this operator manual are examples
only. The actual appearance and design of
these may be slightly different on your system.
For the sake of linguistic simplicity, male and
female patients are referred to as "the patient."
The term "Siemens Service" includes Service
personnel authorized by Siemens.

Configuration
The operator manual supports you when
working with the Spectroscopy task card. It
focuses on completing typical actions quickly
and easily. A light bulb identifies special
remarks.
A complete description for operating the
syngo MR software is included in the exten-
sive Online Help. To select Online Help, press
the F1 key on your keyboard or click the Help
button in the active dialog window.

9
Introduction

Please observe the safety chapter in the

syngo MR Operator Manual during your daily
work.
→ Chapter A 1, Safety instructions

Intended use
Your MAGNETOM system is designed for use as
a diagnostic magnetic resonance system. It
generates transverse, sagittal, coronal and
oblique slice images, spectroscopy images
and/or spectra and displays the inner struc-
tures and/or functions of the head, body, or
the extremities. Depending on the region of
interest, contrast agents may be used. These
images and/or spectra when interpreted by a
trained physician yield information that may
assist in diagnosis.
Your MAGNETOM system may also be used for
imaging during interventional procedures
when performed with MR-compatible devices
such as, in room display and MR-safe biopsy
needles.
The MAGNETOM is not a measurement device
as defined by the medical product guidelines.
Measured values obtained are for informa-
tional purposes and cannot be used only as the
basis for diagnosis.

10
Authorized operating personnel
The MAGNETOM MR system must be operated
according to the intended use and only by
qualified persons with the necessary knowl-
edge in accord with country-specific regula-
tions, e.g. physicians, trained radiological
technicians or technologists, subsequent to
the necessary user training.
This user training has to include basics in MR
technology as well as safe handling of MR sys-
tems. The user has to be familiar with potential
hazard and safety guidelines the same way he
is familiar with emergency and rescue scenar-
ios. In addition, the user has to have read and
understood the contents of the operator man-
ual.

Key emphasis of this manual:

❏ General workflow for measurements and
evaluation in MR spectroscopy based on
two typical 1H MRS examinations of the
head.
❏ Workflow of a breast examination with
syngo GRACE
❏ Distinctive features of the special examina-
tions prostate1H, muscle31P
❏ Protocol management and data export
(DICOM Tool)

11
Basics

Focus in MR spectroscopy (MRS)

In healthy tissue, metabolites are present in
tissue typical equilibrium concentrations.
Stress, functional interferences or diseases
lead to shifts in concentration. These can be
proven non-invasively with MRS by using local-
ized spectra.
❏ Use:
– Evaluation of the cell metabolism
(in-vitro and in-vivo examinations)
– Checking the course of therapy
– Clarifying ambiguous reports from
MR imaging

Localization techniques
An essential prerequisite for MRS used with
humans is a reliable localization. Two tech-
niques are used for allocating the spectra
signals with the anatomically given volume.

Single Voxel Spectroscopy (SVS)

During SVS only a limited volume of interest
(VOI) is acquired. A single spectrum is
obtained.
❏ SVS technique applications:
– 1H MRS of the brain, for examining focal
pathologies (e.g., tumors). Additional
measurement of a comparison spectrum
from a healthy brain areal.

12
Chemical Shift Imaging (CSI)
The measurement volume comprises several
voxels (2D slice or CSI 3D slab). You obtain a
spectra matrix.
❏ Applying CSI technology:
– 1H MRS of the brain or the prostate
– 31P MRS of the muscle, heart or liver
(31P head for 3 Tesla only)
– Examination of multifocal pathologies
(e.g. multiple sclerosis)
– Examination of areas that do not allow
delineation (e.g. determining the epilep-
tic focus)

Spectra and anatomical position

A clinical MRS examination always includes
MR imaging. The joint display of MR spectra
with MR images shows the anatomical loca-
tion of the selected spectroscopy measure-
ment volume.

13
Measurement

Overview of spectroscopy
measurements
We are showing two typical 1H spectroscopy
measurements: SVS and CSI.

Preparation Measurement

Positioning patient Generating the mea-

and coils surement program
→ Page 16 → Page 17

Registering the Measuring/planning

patient reference images
→ Page 16 → Page 18 ff

Planning the
examination volume
→ Page 22 ff

Manual
adjustment
→ Page 25 ff

Measuring raw data

→ Page 30

Our examples will be based on examinations

of the head. Special characteristics of prostate
examinations and other special applications
are included in the respective chapters of this
manual.

14
Evaluation

→ Page 32 ff

15
Measurement

Positioning patient and coils

The preparations for spectroscopy measure-
ments are the same as those for imaging mea-
surements.
✧ Position the coils on the patient table.

Examination region Coils

1H MRS head TxRx_Head or Head
Matrix coil (matrix coil
mode CP) + Spine
Matrix coil

✧ Position the body region of the patient to be

measured in the allocated coil.
✧ Subsequently, determine the center of the
measurement field and move the table into
the magnet isocenter.
✧ Register the patient.
✧ During registration, select the Head_1H
examination. (under Study)

Please note:
This is how you ensure correct spatial alloca-
tion of spectra to reference images:
❏ Ensure that the reference images and
spectra are measured without temporary
repositioning.
❏ Instruct the patient not to move at all if
possible during the entire examination
(including measurement pauses).

16
Generating the measurement
program
You can now start selecting the protocols for
the measurement.
✧ Compile a suitable measurement program.

Example SVS

Example CSI
❏ csi_se...:
2D hybrid CSI with spin echo
❏ ..._135:
echo time in ms

17
Measurement

MRS with scan@center

The scan@center approach ensures optimal
acquisition in the magnet isocenter (highest
field homogeneity). The accurate spatial allo-
cation between spectra and images remains
intact.
❏ scan@center in routine imaging:
During imaging, you can plan isocentric mea-
surements in distortion-corrected reference
images (DIS2D) for different measurement
regions. As a result, MR images are generated
at different table positions.
❏ scan@center in MRS:
To plan spectroscopy and for post-processing
you need, however, non-distortion corrected
images (ND) in the three main orientations.
Spectroscopy measurements have to be per-
formed at the same table position as the
ND images used for planning.

When performing spectroscopy after a routine

imaging examination, the existing images are
generally used to plan the measurement:
If you already know at the beginning of the
examination that a spectroscopy measure-
ment will follow, you can deselect the Posi-
tioning mode ISO prior to measuring the ref-
erence images.

18
 Planning in non-isocentric
reference images
Centrally localized images (DIS2D) of the
examination region from the same table posi-
tion are available.
✧ Select a reference image with high contrast
in the graphic slice positioning (GSP).
✧ Open a spectroscopy protocol.
All images of the selected series are reloaded
as ND images into the GSP. Images of different
orientations (DIS2D) are automatically
unloaded from the GSP.

ND ND ND
TP 0 TP 0 TP 0

If ND images with different orientations are

available from the current examination, you
can load them directly from the program con-
trol.
You can also generate a new series with
ND images from suitable, distortion-corrected
images. (Menu: Evaluation > Inverse 2D
Distortion Correction)

19
Measurement

Planning in isocentric reference

images
All images (DIS2D) come from different table
positions.
✧ Select a reference image with high contrast
in the GSP.
✧ Open a spectroscopy protocol.
Images that have a table position other than
the selected reference image, are automati-
cally removed from the GSP. The selected refer-
ence image is converted into a ND image.

DIS2D DIS2D
TP H50 DIS2D
TP F229 TP F629

✧ Measure additional localizers or reference

images with additional orientations
(ND images).

20
Measure scan@center reference
images
Centrally localized images of the examination
region do not exist. Use the scan@center local-
izers to measure ND images in the isocenter
which are optimally suited for planning and
post-processing in spectroscopy.
✧ Select a reference image with high contrast
in the GSP.
✧ Open a spectroscopy localizer (local-
izer@center or localizer_5@center).
✧ Position the slices in the reference image.
✧ Start the measurement of the localizer.
The patient table automatically moves into the
isocenter. The ND images are measured.
✧ Load the measured reference images into
the segments of the GSP.
The measurement object (VOI/CSI slice) is
shown.

Example SVS

21
Measurement

CSI: Transfer slice positioning

Prerequisite: Reference images with a CSI slice
are shown!
The CSI slice to be planned has to match the
slice position and orientation of the reference
images.
✧ Look for the reference image including the
anatomical region of interest.
✧ Change the display of the reference image
until it is optimal for planning the examina-
tion.
✧ Select the reference image.

✧ Transfer the slice positioning of the refer-

ence image to the CSI slice.
(Menu: Image tools > Copy Image
Position)
The center of the CSI slice is shifted perpendic-
ularly into the plane of the reference image.
The orientation of the CSI slice corresponds
now to the slice orientation of the reference
image.
For controlling the position of the measure-
ment volume in adjacent reference images:
Menu: Scroll > Nearest.

22
Positioning the CSI slice
Both position and size of the CSI slice have to
be adjusted to the anatomical characteristics
of the patient.
✧ Adjust the FoV and VOI.

❏ FoV: large enough to avoid overfolding.

❏ VOI: coverage of the entire area of interest.

Please note:
You can still change the position of the CSI
slice in the predefined plane (“in-plane”).

In case the CSI protocol uses an interpolated

matrix, you are able to adjust the screen dis-
play. (Menu: View > CSI Matrix > Interpo-
lated Matrix)

23
Measurement

CSI: Suppressing interference

signals
For CSI measurements with a spin echo
sequence, we recommend to suppress signal
contributions outside the VOI (Outer Volume
Suppression, OVS).

In the Geometry parameter card

✧ Select Fully excited VOI.
All metabolites of interest are uniformly
excited in the VOI selected. Additionally,
4 saturation regions are positioned automati-
cally (are not shown).
✧ Suppress interfering signal contributions.
For this purpose, arrange up to 8 freely posi-
tionable saturation regions about the VOI (sat-
isfactory fat suppression)

Typical positioning in the head:

4 saturation regions for covering the skull cap,
including 2 transverse saturation regions for
suppressing venous and arterial flow.

24
Optional: Starting protocol
adjustments
Semi-automatic adjustments are recom-
mended for difficult anatomical regions
(e.g.flow, vessels, jumps in susceptibility):
You can check the shim status prior to the
spectroscopy measurement and improve it, if
necessary.
✧ Menu: Options > Adjustments subtask
card Show.

✧ Start with the manual adjustment.

(Adjust All)
All protocol adjustments are performed (as dis-
played in the information window).

25
Measurement

Optional: Shimming interactively

The shim quality is particularly important for
spectroscopy examinations. Use interactive
shimming for checking and improving the
examination. By changing the shim currents
you are able to optimize the results (FWHM,
T2*).

Interactive shim subtask card

✧ Start the shim. (Measure)
An infinite measurement is performed with
the currently set shim parameters.

26
✧ Monitor the results for FWHM and T2*.
❏ FWHM [Hz]: as small as possible
(SVS: 8−13 Hz, CSI: 8−15 Hz, at 1.5 T)
❏ T2*: depends on voxel size and the
metabolites contained within; as large as
possible
✧ End the measurement as soon as you are
satisfied with the results. (Stop)
Otherwise: → Page 27, Optional: Improving
shim results
✧ Close the dialog window.
✧ Start the spectroscopy measurement.
Continue: → Page 30, Measuring raw data

Optional: Improving shim results

In case the results for FWHM and T2* are not
satisfactory, you can improve the homogene-
ity of the magnetic field by changing the shim
currents.
✧ Change the gradient offset for one shim
channel.

27
Measurement

Interactive shim subtask card

Example Channel X, “+” key
✧ Monitor FWHM and T2*.
If the results get worse:
✧ Use the best shim results of the current
measurement (Best Shim).
✧ Change the gradient offset in the other
direction (“–” key).
If the results for FWHM and T2 * continue to be
unsatisfactory:
✧ Repeat the steps for the other channels
(Y, Z).

28
As soon as you are satisfied with the results:
✧ End the measurement. (Stop)
✧ Apply the shim results to the following
spectroscopy measurement. (Apply)

Optional: Adjusting the frequency

Whenever you change shim currents, a “?”
appears in the Frequency (syst) field. This
means that the frequency still needs adjust-
ment (if it is not done manually, the system
handles it automatically)

Frequency subtask card

29
Measurement

✧ Start the frequency adjustment.

(Go)
✧ Monitor the tolerance parameter “Diff [Hz]”.
❏ Optimal frequency: Diff [Hz] = 0 +/− 2 Hz
✧ Repeat the adjustment until you obtain a
satisfactory value for “Diff [Hz]”.
✧ Transfer the frequency determined to the
measurement system. (Close)
You can now begin with the spectroscopy
measurement.

Measuring raw data

Prerequisite: Examination volume is planned!
You are starting to generate the spectroscopy
raw data—using automatic adjustment (man-
ual adjustment → Page 25). During the mea-
surement, you are able to monitor the raw sig-
nal in the Inline Display and control the
measurement accordingly.
✧ Start the measurement.
All adjustments required are performed auto-
matically prior to the measurement. For most
applications, the currently determined default
values of the adjustment configuration are
considered optimal.

30
✧ Open the inline display.
(menu: View > Inline Display)

2 3

(1) Accumulated magnitude spectrum

(2) Magnitude time signal of the current
acquisition
(3) Magnitude spectrum of the current
acquisition
For CSI measurements in the Long term aver-
aging mode, the Inline Display shows the cur-
rent averaging performed by the measure-
ment.

After the measurement, the spectroscopy raw

data and the reference images are automati-
cally stored to the patient database (as shown
by the icons).

Icons for reference images and spectroscopy

raw data in the Patient Browser.

31
Evaluation

Overview of syngo spectroscopy

evaluations
The results of a syngo spectroscopy evaluation
are spectra from the voxels of your measure-
ment volume. The interpretation of these
spectra provides information regarding the
existence, distribution and ratio of diagnosti-
cally relevant metabolites of the region under
examination.

Evaluation

Displaying spectra
→ Page 33

Changing displays
→ Page 34 ff

Interactively post-processing
raw data
→ Page 41 ff

Post-processing CSI data

→ Page 46

Documenting results
→ Page 53 ff

Please note:
In-vivo Siemens post-processing protocols
for 1H MRS raw data do not include a lactate
signal.

32
CAUTION
Selection of unsuitable evaluation parame-
ters!
Artifacts in the spectrum (additional or
covered lines)
✧ Ensure that interactive evaluations are
handled by experts.

Displaying spectra (example: CSI)

Prerequisite: CSI raw data are measured!
You would like to evaluate the voxels of inter-
est in the CSI slice and display the associated
spectra.
✧ Load the raw data into the Spectroscopy
task card (double-click the raw data icon).

33
Evaluation

The reference images from the graphic slice

positioning and the CSI slice are shown.
The raw data of the active voxel (blue) are
automatically evaluated with the appropriate
post-processing protocol.
The resulting spectrum is shown together with
the associated stamp reference images.
✧ Evaluate the voxels of interest in the CSI
slice. (Click voxel)
The associated spectrum is displayed immedi-
ately.
For CSI data:
(1) Set mode “Single data Set”.
(2) Use the protocol for all spectra seg-
ments. (Menu: Protocols > Keep
Common)

Select another CSI slice

(example: 3D-CSI)
In place of the current CSI slice you would like
to select another diagnostically relevant slice
for evaluation within the CSI 3D slab.
✧ Menu: Postprocessing > 3D CSI Selection.

34
✧ Scroll through the CSI volume until the
desired CSI slice is displayed. (Plane num-
ber)
The spectrum in the active segment is newly
calculated. The matching reference image is
displayed (prerequisites: Auto selection
mode is selected).
✧ If required, change the main orientation of
the slice. (Main orientation)
The selection of the active voxel remains
unchanged.

(3)

(1)

(4)
(2)
CSI 3D slab:
(1) selected CSI slice (“Tra”)
(2) after changing to “Sag”
(3) after changing to “Cor”
(4) active voxel (is retained)

35
Evaluation

Look for a suitable reference image

If the displayed reference images do not show
the anatomical region of interest, select other
reference images for syngo spectroscopy eval-
uation.
✧ Look for the reference image including the
anatomical region of interest.

When scrolling through reference images, the

most suitable CSI slice is selected
(Prerequisites: Auto selection mode is
selected).
Reference images from another
measurement: Selecting from the Patient
Browser (Prerequisites: same table position,
ND images).
Updating stamp reference images:
in the dialog window Display Parame-
ters, card Signal: Switching on/off Ref-
erence images.

36
CSI: Hiding graphics in reference
images
For easy viewing of anatomical regions of
interest, you would like to hide some of the
graphics shown in the reference images.
✧ Select the desired reference image.
Example: Only VOI and voxel should be dis-
played for evaluation. We recommend that you
hide “Saturation regions”, “Slice intersections”
and “CSI matrix grid”.

✧ Hide interfering graphics.

37
Evaluation

Scaling the display

Some of the peaks in the spectrum are very
small. To improve interpretation of these
peaks, you would like to enlarge them. For this
reason, you are changing the scaling of the
Y-axis.
✧ Select the spectrum where you would like
to scale the display.

✧ Limit the display area for the Y-axis. (Scale)

Cancelling changes: All changes (Reset),
last change (Menu: Signal > Undo Last
Change)

38
 As an alternative to alpha-numeric changes,
use the mouse to change the scaling of the
axes. (Press the left mouse button and drag it
over the spectrum.)
(1) X-axis (range)
(1)
(2) Y-axis (scale)
(2)

before after

Showing peak information

After a curve fit, the curve of the theoretical
spectrum (red fit line) and the default peak
information are superimposed. You would like
to change this display.
✧ Select the spectrum display you want to
change.

39
Evaluation

Example: Integral and name of peak are to be

superimposed, while fit line is to be hidden.

✧ Select the desired peak information.

The peak information is displayed as image
text above each peak.

40
 Performing phase correction
After the evaluation, to improve the spectrum
display, start with interactive post-processing.
To show the positive signals for the metabo-
lites, correct the phase shift as a first step.

Please note:
Selecting improper evaluation parameters
may cause artifacts in the spectrum.

✧ Select the “Phase correction” post-process-

ing step.
✧ Hold down the center button of the mouse
and pull it across the parameter range of
the dialog window.
(1) Changing the constant phase
(1)
(2) Changing the frequency-dependent
(2) phase component

41
Evaluation

before* after

*
Unusual example, happens rarely in clinical
MRS

Adding a peak
Your spectrum shows a peak that is not
included in the theoretical spectrum. For this
reason, you would like to add a peak to the the-
oretical spectrum and recalculate the curve fit.

✧ Select the “Curve fitting” post-processing

step.
✧ Add a peak. (Add...)

42
The Peak Editor opens.

✧ Select the desired peak from the list of Peak

templates (Double-click)
The peak parameters are shown in the Editor.
✧ Accept the desired peak template for the
curve fit. (OK)
The parameters are transferred to the Curve
fitting window.

In the Interactive Postprocessing dialog win-

dow:
✧ Start computation of the curve fit. (Auto-
matic)

43
Evaluation

Saving the post-processing protocol

To save the changes in the current post-pro-
cessing protocol, save it as its own protocol.
In the Save Protocol dialog window.
(Menu: Protocols > Save As)

✧ Open the directory where you would like to

save the protocol.
✧ Assign a name to the protocol. (Input field
“Protocol name”)
✧ Save the protocol as a new customer proto-
col. (Save)
The new customer protocol is now entered
into your database where you may use it any
time.
Siemens protocols

Customer protocols

44
Evaluating raw data with a different
post-processing protocol
If you are not satisfied with the automatically
evaluated spectrum, use another post-process-
ing protocol in your database for raw data eval-
uation.
In the Open Protocol dialog window.
(Menu: Protocols > Open)

✧ Open the directory that contains the

desired post-processing protocol.
✧ Open the desired post-processing protocol.
(Double-click)
The selected post-processing protocol is
applied to the current raw data. The spectrum
in the active segment is replaced by the newly
computed spectrum.

45
Evaluation

Creating a spectral map

Prerequisite: CSI data are available!
You would like to generate an overview map
(= spectral map) from the spectra computed
for the area of interest.
✧ Select the screen segment that will show
the superimposed spectral map.

✧ Press the button for drawing.

✧ Use the mouse and draw a polygon around
the voxels in the reference image you
would like to include in the computation
range (keep the Ctrl and left mouse button
pressed).
✧ Generate the spectral map. (OK)

46
The spectral map is superposed on the refer-
ence image and shown in the active segment.

Left: Computation range

right: Spectral map, zoomed

Reducing the computation range

again: Press the button and draw a
new polygon.
Delete completely with

47
Evaluation

Generating metabolite images

Prerequisite: CSI data are available!
You would like to display the voxel-dependent
intensity ratio of different metabolites within
the area of interest (in this case: epileptic foci)
in a metabolite image.
✧ Select the screen segment for displaying
the metabolite image.

✧ Select the required image metabolic ratio.

(Cho/NAA)
✧ In addition, you can enter the metabolic
combination as numbers. (+Cr)
✧ Select the type of display (color or grey
scale).
✧ Generate the metabolite image. (OK)

48
The metabolite image is displayed on the refer-
ence image and shown in the active segment.

Set the transparency of the overlaid CSI slice

graphic for metabolite images with the refer-
ence image in background. (Display Parame-
ters dialog window, CSI card)
❏ High Transparency:
Anatomy is more pronounced.
❏ Low Transparency:
metabolite image moves in foreground

49
Evaluation

Showing a metabolite movie

When you have overlaid metabolite images in
the spectral segment, you can display a movie;
in this case, the transparency of the metabolite
image can be changed step by step.

✧ Select the direction you want to run the

movie.
✧ Enter the percent per second the transpar-
ency in the movie should change (e.g. 25%)
✧ Start the movie display. (Metabolite
movie)
The transparency of the metabolite image is
alternately raised to 100% and lowered to 0%.

50
Calculating the sum spectrum
Prerequisite: CSI data are available!
Since the anatomical region of interest covers
several voxels, you would like to add the calcu-
lated spectra of this region and display them as
a sum spectrum.
✧ Select the screen segment for displaying
the sum spectrum.
✧ Menu: Postprocessing > Add spectra.

✧ Add the region of interest to the computa-

tion range (User defined)
✧ Generate the sum spectrum. (OK)

Left: Computation range (e.g., tumor region)

right: Sum spectrum

51
Evaluation

Generating a result table

In addition to the spectrum, you would like to
create a table to show the metabolite ratios
with respect to a reference metabolite.
✧ Select the screen segment where you
would like to display the results table.
✧ Menu: Signal > Result Table.

✧ Determine the reference metabolite. You

may also use a metabolite combination,
e.g., Cho+Cr.
The reference metabolite has the value 1.00.
Integral ratios are computed.
✧ Show the results table in the active seg-
ment. (OK)

52
Saving the results table as a text file:
Prior to confirming with OK select the “Store in
text file” option.

Saving results
After the evaluation, you save your results
(spectra, results table, spectral map and/or
metabolite images) as well as the associated
reference images in the patient directory.
✧ Select the result or reference image you
would like to save.

53
Evaluation

✧ Select the data you want to save and con-

firm with OK.
The results are saved as images to the data-
base (inclusive image text and stamp refer-
ence images).
Reference images are saved in their standard
size including the graphics drawn into them
(VOI, CSI matrix grid).

Filming and printing them

To document your evaluation, send your
results and reference images to the virtual film
sheet.

Please note:
Metabolite images in color may be printed
only with a Kodonix color camera or a color
paper printer.

✧ Select the result or reference image you

would like to film or print.

54
✧ Menu: Patient > Copy to Film Sheet.

✧ Select the data you want to document and

confirm with OK.
The selected data are copied to the virtual film
sheet.

55
Evaluation

Examples of spectra 1H MRS

In the following pages we will show you appli-
cation examples of 1H MRS.

SVS: 1H MRS of the brain

Spectrum of healthy (top) and pathological

tissue (bottom, e.g., NAA reduced, lactate
visible)

56
CSI: 1H MRS of the brain

CSI metabolite image

The metabolite image shows healthy and
malignant tissue across the entire slice.

57
Breast

1H MRS SVS for the breast

The application package syngo GRACE uses the
1
H MRS SVS technology for the breast.
The metabolite status in the tumor tissue can
be acquired via choline. Choline concentration
in healthy breast tissue is usually negligible.
An increased choline signal in the spectrum
usually correlates with a positive biopsy result.
❏ Use:
– Differentiation between malignant and
benign tumors
– Monitoring the course of therapy
– Improved identification of possible vital
residues after chemotherapy and preop-
erative intervention
In what follows we discuss the characteristics
of 1H MR SVS for the breast. A full description
of the workflow is located under head exami-
nations. → Page 14

Positioning the patient and the coil

✧ Position the patient in the prone position in
the Breast Matrix Coil.
✧ During registration, select the Breast_1H
examination. (under Study)
✧ Select the appropriate coil element for the
measurement.

58
Quantification with an external reference
A reference solution is present in the coil hous-
ing for quantifying the choline signal. The cho-
line signal is automatically normalized with an
additional measurement of the reference sam-
ple signal.

Quantification with an internal reference

An additional possibility for quantifying the
choline signal consists of an “internal” refer-
ence measurement, that is, in the tumor. For
this purpose, you can perform a fast, non-
water suppressed measurement in the tumor
with an identical voxel position and size.

Please note:
The internal reference method is not consid-
ered clinically sound for controlling the
course of therapies. The behavior of internal
water in the tumor during, e.g., chemother-
apy is largely unknown.

59
Breast

Performing external reference

measurements
For localizing the reference solution:
✧ Open and start the reference localizer.
(Localizer is already positioned on the small
reference bottles.)
✧ Open the reference localizer
svs_se_breast_ref.
✧ Position the voxel fully within the reference
sample.
✧ Start the SVS reference measurement.
A fast SVS measurement without water sup-
pression is performed.

Planning the VOI

✧ For planning, use reference images in three
orientations.
Subtraction images in three orientations are
optimal for accurately covering the tumor.
✧ Position the voxel so it exclusively contains
the tumor.

Optimal positioning

60
Poor positioning, voxel is too large (fat signal is
superimposed on choline signal)

Suppressing interference signals

Suppressing motion artifacts

You can perform an Inline frequency correc-
tion to minimize respiratory motion artifacts.

In the Sequence parameter card

✧ Select Freq. Corrected Accumulation.

61
Breast

In the Contrast/Common parameter card

✧ Ensure that reduced water suppression has
been enabled. (Reduced water suppr.)

Suppressing fat signals

To minimize fat signal, you are able to perform
an Inline spectral fat saturation.

In the Contrast/Common parameter card

✧ Select Lipid suppr. from the Spectral
suppr. list.
✧ Select the bandwidth of the suppression
pulse. (Lipid suppr. BW)
✧ Select the spectral shift of the suppression
pulse. (Lipids s. delta pos.)
To better adjust the voxel to the lesion, you can
position up to 8 saturation slices.

62
Normalizing the choline signal
Prerequisite: Reference data set is available.
You can convert the relative choline concen-
tration to an absolute concentration by com-
puting the ratio of the integrals of the choline
and reference peaks. Use the integral of the
reference sample pulse and compute the ratio
to the choline signal.

✧ Select the “Normalization to reference”

post-processing step.
✧ Enable automatic search for a reference
data set. (Find and load automatically)
✧ Start normalization. (Apply)

63
Breast

Examples of spectra
In the following pages we will show you appli-
cation examples of 1H MRS for the breast.

Tumor spectrum of breast cancer before

chemotherapy. Biopsy correlates with high
choline signal in the spectrum.

64
Tumor spectra in the second cycle (top) and in
the fourth cycle (bottom) of chemotherapy.

65
Prostate

1H MRS CSI for the prostate

1H MRS of the prostate can be used to detect
changes in signal intensity of the citrate
metabolite.
Citrate is an important metabolic product of
the Krebs cycle in the mitochondria of living
cells. Intracellular citrate concentrations are
very low. However, citrate can be detected as
secretion of the healthy prostate. A missing
citrate signal in prostate tissue indicates a
carcinoma.
At the recommended echo time of 120 ms and
B0 = 1.5 T, the spectrum of healthy prostate
tissue shows a strong citrate signal, which is
typically significantly higher than the choline
signal.
→ Page 68, Examples of spectra
However, the citrate/choline signal ratio in the
prostate is subject to regional differences. The
highest ratios were found in the peripheral
zone; in the area of the ureter, however, the
ratio may be reversed even in the healthy pros-
tate. High choline and low citrate signals were
found in cancerous prostate tissue. However,
the spatial inhomogeneity has to be consid-
ered for the evaluation. In addition, research is
currently being conducted on, e.g., the effects
of prostatitis on the signal ratio.
In what follows we discuss the characteristics
of 1H MRS CSI for the prostate. A full descrip-
tion of the workflow is located under head
examinations.
→ Page 14

66
Positioning the patient and coil
✧ Use the Endorectal Coil.
✧ During registration, select the Prostate_1H
examination. (under Study)

Planning the VOI

✧ Position the voxel so it covers the entire
prostate.

Measurement
The measurement protocols are based on a
3D-spin-echo hybrid CSI sequence. This
3D sequence allows you to perform a full pros-
tate examination in one step.

Please note:
The shape of the strong coupling citrate sig-
nal changes depending on the magnetic
field. Therefore, the current measurement
protocol with TE = 120 ms is optimized to
determine the citrate signal at 1.5 T only.

Suppressing fat signals

If combined with “Outer Volume Suppression”
and spectral signal suppression, interference
from fat signals can be effectively reduced.
→ Page 24
→ Page 62

67
Prostate

The following images show the positioning of

free saturation regions using the example of a
1H hybrid CSI measurement of the prostate.

Examples of spectra
In the following pages we will show you
application examples of 1H MRS CSI for the
prostate.

Metabolite image of healthy and pathological

tissue.

68
Spectra of healthy (top) and pathological pros-
tate tissue (bottom).

69
Multi-nucleus

Multinuclear spectroscopy
The application packages “Multinuclear
Support” and “Multinuclear Spectroscopy”
enable measurements and evaluations for
nuclei 7Li, 13C, 19F and 31P. In addition 31P
protocols are available for special applications
regarding muscles (1.5 T and 3 T), head (3 T),
heart and liver (1.5 T).
In what follows we discuss the characteristics
of 31P MRS examinations for the muscles,
heart or liver. A full description of the work-
flow is located under head examinations.
→ Page 14

31
P MRS of the muscle, heart or liver
(31P head protocols for 3 Tesla only)
31P MRS acquires the most important energy
carriers of the cell such as ATP, creatine phos-
phate and inorganic phosphate. Based on the
relative concentrations of these phosphorous
metabolites, information can be collected
regarding the energy state of the cell.

Please note:
A physiologically triggered measurement via
ECG signal is required for 31P MRS of the
heart.

70
Positioning the patient and coil
Siemens provides a heart/liver coil for 1.5 T
systems. For 3 T systems, coils from other
manufacturers are used.
In what follows, the use of the heart/liver coil
is described. Coils of other manufacturers are
operated in a similar way.
The heart/liver coil has dual resonance, i.e., it
is resonant for both 1H and 31P frequencies
(63.6 MHz or 25.7 MHz; at 1.5 T) and can be
toggled between the two resonance frequen-
cies. (Coils from other manufacturers also usu-
ally have dual resonance.)
The heart/liver coil is used for both acquiring
31
P spectra as well as anatomical reference
images. In addition, the coil is used for fre-
quency adjustment and for shimming based
on the 1H signal.

Please note:
Do not connect another local coil while the
heart/liver coil is connected.

71
Multi-nucleus

Planning the VOI

31P MRS protocols use either the FID or the
CSI FID sequence. The signal is not localized by
the FID sequence. It comes from the entire
sensitive region of the coil. With CSI FID proto-
cols, data acquisition is performed immedi-
ately after localization via slice selection and
phase encoding.
An additional VOI planning for suppressing
interference signals is not necessary.

Please note:
Due to the absence of a volume selection,
a sufficiently large FoV should be selected for
the CSI FID sequence to prevent aliasing
artifacts.
This applies to each spatial direction,
because in the CSI FID sequence each spatial
direction is resolved via phase encoding.

Setting the measurement

parameters

In the Sequence/Nuclei parameter card

✧ Set the requested parameters.

72
Multinuclear frequency adjustment
You determine the exact resonance frequency
for the nucleus determined by the protocol.
✧ Menu: Options > Adjustments subtask
card x Frequency.

✧ Set the adjustment parameters.

✧ Ensure that the bandwidth is large enough
to receive the signal.
To allow for sufficient signal detection,
increase the number of averages for weak sig-
nals.
✧ Start the frequency adjustment. (Go)

73
Multi-nucleus

Multinuclear transmitter
adjustment
Since the signal strength is minimal, transmit
adjustment measurements are not possible
during multinuclear measurements. However,
you can define a reference amplitude and
apply it as the new system reference ampli-
tude.
✧ Menu: Options > Adjustments subtask
card x Transmitter.

Subtask card x Transmitter

74
Examples of spectra
We are showing you applications of 31P MRS
for the heart.

Spectra of healthy tissue (top) and a metabo-

lite image of a myocardial infarction (bottom).

75
Protocol management

In addition to the post-processing protocols by

Siemens, you are able to generate your own
evaluation protocols. These will be filed as cus-
tomer protocols in your protocol database.

Creating a new protocol directory

You are able to group customer protocols by
starting a new protocol directory.
In the Save Protocol dialog window.
(Menu: Protocols > Save)

You can create new protocol directories on the

system type or type of nucleus level.
✧ Select “protocol tree” to generate a new
directory on the system type level.
✧ Select a system type directory to generate a
directory on the type of nucleus level.
✧ Enter a name for the new directory.
(Input field “Protocol name”)
✧ Open the new protocol directory. (Open)

76
The new protocol directory is added to the
directory structure.

Please note:
The new protocol directory is created on a
temporary basis only! If you do not store a
post-processing protocol in the directory, it
will be removed again.

Importing customer protocols

To use other than your own protocols on your
system, import them to your local database.
In the Import Protocol(s) dialog window.
(Menu: Protocols > Import)

✧ Open the directory for importing customer

protocols. (Import from:)
✧ Select the protocols you want to import.
✧ Import the selected protocols. (Import)

77
Protocol management

Exporting customer protocols

To provide other users with your own protocols
or use them on other systems, export your pro-
tocols from the database.
In the Export Protocol(s) dialog window.
(Menu: Protocol > Export...)

✧ Open the directory for exporting customer

protocols.
✧ Select the protocols you want to export.
✧ Start to export. (Export)
✧ Go to the following dialog window and
select the desired destination directory
(“C:\....” on your hard disk or a drive with
exchangeable mass medium, e.g.,
a diskette).
✧ Export the selected protocols. (Export)
The protocols generated include the data
extension “pro”.

78
Delete customer protocols
To keep the protocol database organized,
delete customer protocols that are no longer
required.
In the Delete Protocol(s) dialog window.
(Menu: Protocols > Delete)

✧ Open the directory for deleting customer

protocols.
✧ Select the protocols you want to delete.
✧ Delete the selected protocols. (Delete)
✧ For safety purposes, you have to confirm
the deletion.

79
Exporting raw data

For evaluation with other programs, you can

send the spectroscopy raw data to external
computers.

Exporting raw data in DICOM

format
The DICOM Tools function enables you to
send or export spectroscopy raw data in the
DICOM format.
In the Patient Browser.

✧ Select the raw data you would like to

export.

80
By selecting a series or study, you are able to
export the spectroscopy raw data contained in
it.
✧ Select Applications > DICOM Tools > Send
(Export) MR Spectroscopy.

Exporting raw data as an ASCII file

In the Spectroscopy task card.
✧ Select the spectrum whose raw data you
would like to export.
In the Export Rawdata in Ascii File dialog
window. (Menu: Options > Export raw data)

✧ Select the desired destination medium and

directory. (Export to:)

81
Exporting raw data

Please note:
You can only export small raw data sets on
floppy, e.g., SVS raw data.

✧ Start exporting. (Export)

The raw data are being exported.
The ASCII file generated includes the data
extension “.rda”.

82
© Siemens AG 2008
Order number
MR-05002.630.08.01.02
Printed in Germany
03/2008

Siemens AG Contact:
Wittelsbacherplatz 2 Siemens AG
D-80333 München Medical Solutions
Germany Henkestr. 127
D-91052 Erlangen
Germany
Telephone: +49 9131 840
www.siemens.com/medical

www.siemens.com/medical