1. ACRIN-6684 - MRS data acquisition and Raw Data Handling Instructions – For GE Data

2. In vivo MR Spectroscopy
Representative MRS of a normal human
NAA
Cho Cr
Lipids,
macromolecules
Glu/
Gln MI 2

3. 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 3

4. Lac
NAA Cr
Cho
Lactate (Lac) at 1.3 ppm, inverted at 144ms: produced by an anaerobic metabolism, found in tumor containing zones of necrosis

5. The Sequence
3D Volumetric Spectroscopy preferred 2D CSI Spectroscopy is acceptable

6. 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.

7. Suboptimal Voxel Placement
Proximity to sinuses can result in signal broadening and susceptibility artifacts
Proximity to scull can result in contaminating lipid signal

8. Parameters TR ~1100 ms and TE 144 ms,
Phase encoding arrays 12 x 12 x 8:
For GE scanners: Freq = 12, Phase = 12 and Locs per Slab = 8
FOV > 160 mm2
Click Graphic Rx and select
Spacing: 10
Voxel Thickness: e.g. 60.0
Make smaller than the width
of the 8 slabs

9. Saturation Bands
Click SAT and place up to 6 SAT bands to eliminate signal from subcutaneous fat
Thickness of SAT bands 4 – 5 cm

10. Parameters
To accomplish partial or elliptical k-space sampling reduce NEX below 1 (there will be a drop down menu) which will reduce the acquisition time.
Prescan is recommended before the acquisition to check for full width at half maximum (FWHM)

11. 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
Better signal separation, thus better quantification of metabolites
Better water suppression
Suboptimal shimming 11

12. Saving the dicom data In Browser, select spectroscopy exam
Click on Functool

13. In Browser, highlight the image series used for localizing spectroscopy
Click OK

14. Select Protocol - 2D Brain

15. Make screen saves from image and spectroscopy voxels

16. To do that: right click on the image
A scroll down window will appear
Select save screen shot

17. Repeat for every slice

18. How to save raw data (p files)
The GE spectroscopy data is saved as so-called p file on the scanner in a directory /usr/g/mrraw
How to make sure that p-files will not be overwritten.
On the MRI console, go to the Browser
Right mouse-click on the background
A scroll down window appears, select Service tools and  Command Window
 In the terminal window that pops up type: cd /usr/g/mrraw (this is the directory in which all p-files are temporally stored)
 Type: ls –ltr (this command lists all p-files including time stamps in chronological order)
Command Tool

19. How to save raw data (p files)
 Type: mkdir backup (this generates a backup folder in which p-files can be stored, this only needs to be done once)
 Type: cp Pxxxxx.7 backup (this command copies the p-file in your backup directory. The x’s represent the 5 digit code for the p file you are interested in.)
 Type: cd backup
Type: mv Pxxxxx.7 PatientID.date.Pxxxxx.7 (this command renames your p file, this way you make sure that the file will not be overwritten during later experiments.)