External Email - Use Caution
Thanks 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
????????????????????
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
????????????????????
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Dincer, Aylin -
Douglas N. Greve