acrin-6689 - acrin-6689 - mrs data acquisition and raw data handling instructions – for siemens...
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ACRIN-6689ACRIN-6689 - - MRS data acquisition and Raw
Data Handling Instructions –
For Siemens Data
In vivoIn vivo MR Spectroscopy MR Spectroscopy
Representative MRS of a normal human brain @3T
NAA
Glu/Gln
Cho Cr
MI
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
Lactate (Lac) at 1.3 ppm, inverted at 144ms: produced by an anaerobic metabolism, found in tumor containing zones of necrosis
1000 950 900 850 800
-1.00E+008
0.00E+000
1.00E+008
2.00E+008
3.00E+008
Y A
xis
Title
X Axis Title
fft(real)
/ ppm
1000 950 900 850 800
-1.00E+008
0.00E+000
1.00E+008
2.00E+008
3.00E+008
Y A
xis
Title
X Axis Title
fft(real)
/ ppm
Lac
NAA
Cr
Cho
The Sequence The Sequence
3D chemical shift imaging using a Point-resolved spectroscopy (PRESS) excitation pulse sequence.
3D Volumetric Spectroscopy preferred 2D CSI Spectroscopy is acceptable
Optimal Voxel PlacementOptimal 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 Suboptimal Voxel PlacementPlacement
Proximity to sinuses can result in signal broadening and susceptibility artifacts
Proximity to scull can result in contaminating lipid signal
3D MRSI Parameters3D MRSI ParametersTE 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.
ShimmingShimming “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
Shimming on SiemensShimming on Siemens
Manual Shimming on Manual Shimming on SiemensSiemens
Hit the “Show” tabThen “Invalidate All”“Adjust All”Wait a couple of minutes until it says “Adjustments finished”
Hit the “Show” tabThen “Invalidate All”“Adjust All”Wait a couple of minutes until it says “Adjustments finished”
Hit the “Interactive Shim” tabThen 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)
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Saturation BandsSaturation BandsClick SAT and place up to 10 SAT bands
around the voxel to suppress signals from lipid/fat
Saving the Data in .rda Saving the Data in .rda format format
•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.
BTW: Please select Single Dataset Mode!
Go to the top of the screen Click on “Patient” Dropdown menu will appear“Save data”
•Select first option, Selected results and 3 reference images (shown above)•This will save the spectrum
and corresponding images in a DICOM format
Go to a difference slice and repeat the process
In order to use a different slice:Right click on the ImageA scroll down window will appear Select 3D CSI Selection
Under 3D CSI Selection:Choose Plane number
Saving the Data in .rda Saving the Data in .rda format format
Click on Options – export raw data (shown above).
Saving the Data in .rda Saving the Data in .rda format format
1. The previous command (Options-export raw data), will open this new window. By default the directory is C:\Temp (leave default)
2. .Save File name as “ACRINcase#_timepointXweeks”• Example: case09_16weeks.rda
3. Click Export
1. 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.
2. 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…”)
3. Find your folder: It will be identified by your ACRIN Institution Name Contact Jim Gimpel at ACRIN at [email protected] for assistance
4. Store your file in the folder:(BE SURE YOU HAVE NAMED IT as Case#_Timepoint)
Sending P-Files to ACRINSending P-Files to ACRIN