1. ACRIN-6689 - MRS data acquisition and Raw Data Handling Instructions – For Siemens 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 chemical shift imaging using a Point-resolved spectroscopy (PRESS) excitation pulse 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. 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.

9. 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 9

10. Shimming on Siemens

11. Manual Shimming on Siemens
Hit the “Show” tab
Then “Invalidate All”
“Adjust All”
Wait a couple of minutes until it says “Adjustments finished”

12. 2. 1. 3. 4. 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) 2. 1. 3. 4.

13. Saturation Bands
Click SAT and place up to 10 SAT bands around the voxel to suppress signals from lipid/fat

14. Saving the Data in .rda format

15. 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.
Active box represented by a blue box

16. BTW: Please select Single Dataset Mode!

17. Go to the top of the screen Click on “Patient”
Dropdown menu will appear
“Save data”
Active box represented by a blue box

18. This will save the spectrum and corresponding images in a DICOM format
Gray box appears
Select first option, Selected results and 3 reference images (shown above)
This will save the spectrum and corresponding images in a DICOM format

19. Go to a difference slice and repeat the process
Gray box appears

20. In order to use a different slice: Right click on the Image
A scroll down window will appear
Select 3D CSI Selection
Gray box appears

21. Gray box appears
Under 3D CSI Selection:
Choose Plane number

22. Saving the Data in .rda format
Click on Options – export raw data (shown above).

23. Saving the Data in .rda format
The previous command (Options-export raw data), will open this new window. By default the directory is C:\Temp (leave default)
.Save File name as “ACRINcase#_timepointXweeks”
Example: case09_16weeks.rda
Click Export

24. Sending P-Files to ACRIN
Be sure the rda file is named “Case#_ Timepoint”
For example: “4200_case15_baseline.rda” or “4200_case09_week16.rda”
Again, this MUST be the ACRIN CASE NUMBER assigned at registration.
Login to ACRIN via ftp:
On your web browser, go to ftp://xray.acrin.org
User Name: (CONTACT ACRIN FOR USERNAME)
Password: (CONTACT ACRIN FOR PASSWORD)
(If not prompted, click file, “Login As…”)
Find your folder:
It will be identified by your ACRIN Institution Name
Contact Jim Gimpel at ACRIN at for assistance
Store your file in the folder:
(BE SURE YOU HAVE NAMED IT as Case#_Timepoint)