On 3/24/2020 6:11 PM, Dincer, Aylin wrote:
External Email - Use Caution
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)
As I mentioned below, don't do it this way if you want the gtm stats to
have 1 in the reference region.
2) concatenating the frames as suggested in the previous response (ref region
SUVR about 1.34)
This was not what what was suggested.
3) running with the SUV image (ref region SUVR about 1.003).
I think this is what I suggested. You have two reference regions (8 and
47) but you only list one value above. My guess is that the other is
going to be .997 so that they average to 1
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
_______________________
Message: 11
Date: Fri, 6 Mar 2020 16:59:53 -0500
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer reference region
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8c262861-3272-151b-ae18-906898408...@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:
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" <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer reference region
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@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
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