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

In vivo MR Spectroscopy Representative MRS of a normal human brain @3T NAA Cho Cr Lipids, macromolecules Glu/ Gln MI 2

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

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

The 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

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

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

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)

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

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

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

Select Protocol - 2D Brain

Make screen saves from image and spectroscopy voxels

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

Repeat for every slice

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

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.)