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)

1.

2.

3.

4.

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 jgimpel@acr-arrs.org 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