ACRIN-6684
- MRS data acquisition and Raw Data Handling
Instructions –
For Siemens Data
In vivo MR Spectroscopy
Representative MRS of4000
a normal human brain @3T
NAA
Y Axis Title
3000
2000
Cho
1000
Cr
Glu/
Gln
MI
0
600
X Axis Title
Lipids,
macromolecules

Proton MRS is able to detect the following metabolites:
N-Acetyl Aspartate (NAA) at 2 ppm: Marker of
neuronal density and viability
 Creatine (Cr) at 3 ppm: Energy metabolism, generation
of ATP
 Choline (Cho) at 3.2 ppm: Pathological alterations in
membrane turnover, increased in tumors
 Lipids (Lip) between 0.8 – 1.5 ppm: Breakdown of
tissue, elevated in brain tumors - lipids indicate
necrosis

fft(real)
3.00E+008
Cho
NAA
Y Axis Title
2.00E+008
Cr
1.00E+008
Lac
0.00E+000
-1.00E+008
1000
950
900
850
800
X Axis Title
 / ppm

Lactate (Lac) at 1.3 ppm, inverted at 144ms:
produced by an anaerobic metabolism, found
in tumor containing zones of necrosis
The Sequence


3D chemical shift imaging using a Pointresolved spectroscopy (PRESS) excitation
pulse sequence.
3D Volumetric Spectroscopy preferred 2D
CSI Spectroscopy is acceptable
Optimal Voxel Placement

The ROI will be placed at the center of the
enhancing tumor covering the lesion and the
normal brain as much as possible but excluding the
subcutaneous fat and sinuses.
Suboptimal Voxel Placement


Proximity to sinuses can result in signal
broadening and susceptibility artifacts
Proximity to scull can result in contaminating
lipid signal
3D MRSI Parameters
 TE
144 ms, TR 1140 ms,
 FOV > 160 mm2,
 Phase encoding arrays 12 x 12 x 8
 Numbers of Acquisitions: 1
 Spatial zero-filling to 16 x 16 x 8 phase encoding arrays will
result in an individual voxel size of 1 x 1 x 1 cm3.
 Approximate imaging time: ~6 min utilizing elliptical k-space
sampling k-space sampling
 Manual shimming is recommended before the acquisition to
obtain the best magnetic field homogeneity.
Shimming
“Shimming” = adjusting the magnetic field to make it more
homogeneous
 1.5T: Signal line width or full width at half maximum (FWHM): <15
Hz for 3D MRSI
 3 T: FWHM < 25 Hz for 3D MRSI

Cho&Cr

NAA
Suboptimal shimming


Better signal separation, thus better
quantification of metabolites
Better water suppression
Shimming on Siemens
Manual Shimming on Siemens
Hit the “Show” tab
Then “Invalidate All”
“Adjust All”
Wait a couple of minutes until it
says “Adjustments finished”
2.
Hit the “Interactive Shim” tab
Then hit “Measure” (1)
Numbers will begin to scroll on the above white
box (2)
You can alter the shim by changing Z, then Y, then
X. Do this slowly, only a couple of increments at a
time, then start with z again …
Stop (3) and Apply (4)
1.
3.
4.
Saturation Bands
 Click
SAT and place up to 10 SAT bands around the voxel to
suppress signals from lipid/fat
Saving the Data in .rda format
•The spectrum appears in one of the
quadrants
•Note: if another window appears
asking you to select a protocol for the
spectrum, just select any of the
protocols listed and click OK.
BTW: Please select Single
Dataset Mode!
Go to the top of the screen Click
on “Patient”
Dropdown menu will appear
“Save data”
•Select first option, Selected results and
3 reference images (shown above)
•This will save the spectrum and
corresponding images in a DICOM
format
Go to a difference slice and repeat the
process
In order to use a different slice:
Right click on the Image
A scroll down window will appear
Select 3D CSI Selection
Under 3D CSI Selection:
Choose Plane number
Saving the Data in .rda format

Click on Options – export raw data (shown above).
Saving the Data in .rda format
1. The previous command (Options-export raw data), will
open this new window. By default the directory is
C:\Temp (leave default)
2. .Save File name as “ACRINcase#_timepointXweeks”
• For example: case15_baseline.rdaor case09_16weeks.rda
3. Click Export