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)
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
_______________________
Message: 11
Date: Fri, 6 Mar 2020 16:59:53 -0500
From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer reference region
To: <freesurfer(a)nmr.mgh.harvard.edu>
Message-ID: <8c262861-3272-151b-ae18-9068984084d4(a)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" <dgreve(a)mgh.harvard.edu>
> Subject: Re: [Freesurfer] PetSurfer reference region
> To: <freesurfer(a)nmr.mgh.harvard.edu>
> Message-ID: <64d6089e-f818-e30e-deff-98a812b72636(a)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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