Re: [Freesurfer] PetSurfer reference region

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Hello PetSurfer experts,

We found the SUVR values for the reference region (lh/rh cerebellum cortex) does not equal 1 in the gtm.stat.dat file.

We tried a few things: 1) leaving the PET image as multi-frames (ref region SUVR about 1.34) 2) concatenating the frames as suggested in the previous response (ref region SUVR about 1.34) 3) running with the SUV image (ref region SUVR about 1.003).

I attached the terminal output and the gtm.stat.dat file from the concatenated image run.

Here is the command we ran using v6: mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf 8--seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx .01 --rescale 8 47 -o regmean_gtmpvc_output

Let me know if you have suggestions.

Thanks so much, Aylin

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Message: 11 Date: Fri, 6 Mar 2020 16:59:53 -0500 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer reference region To: freesurfer@nmr.mgh.harvard.edu Message-ID: 8c262861-3272-151b-ae18-9068984084d4@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"

I think the issue is that your input has multiple frames (6). It will compute the scaling from all 6 whereas the gtm.stats file is only from the first frame. Try running it with a single frame. Note that the gtm.nii.gz will have all the frames for each ROI.

On 3/6/2020 3:56 PM, Dincer, Aylin wrote:

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Thanks for the quick reply. I attached the terminal output to this email. We are running this on v6.

Best, Aylin

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Message: 9 Date: Fri, 6 Mar 2020 11:50:51 -0500 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer reference region To: freesurfer@nmr.mgh.harvard.edu Message-ID: 64d6089e-f818-e30e-deff-98a812b72636@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"

I cannot replicate this in either v6 or v7beta. Can you send the terminal output?

On 3/5/2020 1:32 PM, Dincer, Aylin wrote:

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Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but noticed that the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is what we were expecting). The actual SUVR values are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached the stats file (gtm.stats.dat) and below is the command we ran.

mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output

Let me know if you need any more details.

Thanks so much,

Aylin

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Aylin Dincer

Senior Research Technician

NeuroImaging Laboratories

Imaging Core, Benzinger Lab

314-362-3629

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