Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

External Email - Use Caution Found it. Thank you very much! Thanks, ZZ On Apr 26, 2022, 12:28 -0700, Zhener Zhang , wrote: Thank you, Douglas! Is it possible to extract the number of voxels in each segment [of the FreeSurfer DK atlas]? We are hoping to ‘reverse’ the spatial av

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

yes, in the gtm.stats file. See https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer for docs On 4/26/2022 3:29 PM, Zhener Zhang wrote: External Email - Use Caution Thank you, Douglas! Is it possible to extract the number of voxels in each segment [of the FreeSurfer DK atlas]? We are

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

External Email - Use Caution Thank you, Douglas! Is it possible to extract the number of voxels in each segment [of the FreeSurfer DK atlas]? We are hoping to ‘reverse’ the spatial averaging process to get the sum of expression level in each ROI. Thanks, ZZ On Apr 25, 2022, 11:3

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

In that case, it mapping the seg into the pet space (see aux/seg.nii.gz) and just averaging over the voxels in each segment. On 4/25/2022 2:34 PM, Zhener Zhang wrote: External Email - Use Caution Hi Douglas, Thanks! We ran the following for one of our subjects: mri_gtmpvc --i sz

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

External Email - Use Caution Hi Douglas, Thanks! We ran the following for one of our subjects: mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg ~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale --o ~/sz013/gtmpvc.output Thanks, ZZ On Apr 24, 2022, 13:

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

There are several ways it might work depending upon how you ran it. This is why I was asking for your command line. On 4/24/2022 4:46 PM, Zhener Zhang wrote: External Email - Use Caution Hi Douglas, Thank you for the reply! The mri_gtmpvc outputs were expected and there was no reaso

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

External Email - Use Caution Hi Douglas, Thank you for the reply! The mri_gtmpvc outputs were expected and there was no reason for us to suspect that something was wrong. I was just curious as to the general process behind PETSurfer’s ROI-wise value calculation. Was each ROI-wi

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

Can you send your mri_gtmpvc command line? On 4/20/2022 12:50 PM, Zhener Zhang wrote: External Email - Use Caution Hello, I have a question regarding the way ROI-wise values are calculated using PETSurfer. We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively smal

[Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

External Email - Use Caution Hello, I have a question regarding the way ROI-wise values are calculated using PETSurfer. We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small ROI like Putamen has one of the highest values of regional distribution of a PET