ACRIN-6684 - MRS data acquisition and Raw Data Handling Instructions

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

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In vivo MR Spectroscopy
Representative MRS of a normal human brain _at_3T
NAA
Cho
Cr
Lipids, macromolecules
Glu/ Gln
MI
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• 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

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• Lactate (Lac) at 1.3 ppm, inverted at 144ms
  produced by an anaerobic metabolism, found in
  tumor containing zones of necrosis

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The Sequence

• 3D Volumetric Spectroscopy preferred 2D CSI
  Spectroscopy is acceptable

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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.

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Suboptimal Voxel Placement

• Proximity to sinuses can result in signal
  broadening and susceptibility artifacts
• Proximity to scull can result in contaminating
  lipid signal

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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 gt 160 mm2
• Click Graphic Rx and select
• Spacing 10
• Voxel Thickness e.g. 60.0
• Make smaller than the width
• of the 8 slabs

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Saturation Bands

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

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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)

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Shimming

• Shimming adjusting the magnetic field to make
  it more homogeneous
• 1.5T Signal line width or full width at half
  maximum (FWHM) lt15 Hz for 3D MRSI
• 3 T FWHM lt 25 Hz for 3D MRSI

• Better signal separation, thus better
  quantification of metabolites
• Better water suppression

• Suboptimal shimming

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Saving the dicom data

• In Browser, select spectroscopy exam
• Click on Functool

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In Browser, highlight the image series used for
localizing spectroscopy Click OK
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Select Protocol - 2D Brain
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Make screen saves from image and spectroscopy
voxels
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• To do that right click on the image
• A scroll down window will appear
• Select save screen shot

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Repeat for every slice
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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
  temporarily stored)
•  Type ls ltr
• (this command lists all p-files including time
  stamps in chronological order)

Command Tool
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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 xs
  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.)

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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)

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How to transfer the P-Files

• On the right side you see your scanners
  directory and on your left side your own
  computers 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!

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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.

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Sending P-Files to ACRIN

• Rename P file to ACRINCase, TimepointXweeks
• 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
• 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_at_acr-arrs.org for assistance
• Store your file in the folder
• (BE SURE YOU HAVE NAMED IT as Case,Timepoint)