ACRIN-6684
- MRS data acquisition and Raw Data Handling
Instructions –
For GE Data
In vivo MR Spectroscopy
Representative MRS of4 0a0 0normal human brain @3T
NAA
Y A xis T itle
3000
2000
Cho
1000
Cr
Glu/
Gln
MI
0
600
X A x is T itle
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 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
> 160 mm2
 Click Graphic Rx and select
 Spacing: 10
 Voxel Thickness: e.g. 60.0
 FOV
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
Suboptimal shimming


Better signal separation, thus better
quantification of metabolites
Better water suppression
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
Command Tool

In the terminal window that pops up type: cd /usr/g/mrraw
(this is the directory in which all p-files are temporarily stored)

Type: ls –ltr
(this command lists all p-files including time stamps in chronological order)
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.)
How to transfer the P-Files



FIRST: Once isolated, the P-Files will need to be sent from your scanner to a PC
You can use any PC with a network connection to transfer the p-files.
An ftp client is required. The easiest way to transfer the files is by using a program
called WinSCP which can be downloaded free at http://winscp.net/eng/index.php
CONFIGURATION:

Open the program and setup:





Host name: IP address of your MRI scanner
Login and password will be likely sdc and adw2.0
Login: sdc
Password: adw2.0
Protocol: SFTP (allow SCP fallback)
How to transfer the P-Files




On the right side you see your scanner’s directory and on your left side your
own computer’s directory (see below)
Change the directory on the right site to /usr/g/mrraw/backup
Transfer the p-files from that directory to your computer by clicking on the
file, then drag it to a designated data storage folder on your computer (to the
left). A window will pop up, select the option to copy.
Done!
How to transfer the P-Files
TIPS:



Once you have setup that connection you can save the session and you do
not need to remember the IP address, login and password anymore.
Go to session, save session and type in scanner name.
Next time you want to transfer files you can you load the session.
Sending P-Files to ACRIN
1.
Rename P file to “ACRINCase#, TimepointXweeks”


2.
For example: case15_baseline OR case09_16weeks
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


3.
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 Insitution Name
Contact Kesha Smith at ACRIN at ksmith@acr-arrs.org for assistance
4. Store your file in the folder:
(BE SURE YOU HAVE NAMED IT as Case#,Timepoint)