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:
External Email - Use CautionThanks for the quick reply. I attached the terminal output to this email. We are running this on v6.
Best, Aylin
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:
????????External Email - Use Caution
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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