Hi Lorenzo,
I was trying to do this too, and used:
1. mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi $h
--sval-annot $h.yeo.annot
--tval $SUBJECTS_DIR/$s/label/$h.yeo.annot
2. make yeo.gtmseg.ctab - I copied gtmseg.ctab, pasted yeo network ctab at end
(offset LH by 1000, offset RH by 2000) and added column with tissue type
(1=cortex)
ie. 1001 lh_17Networks_1 120 18 134 1
3. gtmseg --s $s --o yeo.gtmseg.mgz
--ctx-annot yeo.annot 1000 2000
--ctab yeo.gtmseg.ctab
4. mri_gtmpvc --i pet.nii.gz --reg template.reg.lta
--psf FWHM --default-seg-merge
--auto-mask PSF .01 --mgx .01
--seg yeo.gtmseg.mgz
--o yeo.gtmpvc.output
This worked for me, but Doug and others can tell you if this should be done
differently.
Best,
Sara
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lorenzo Pini
[pini.loren...@gmail.com]
Sent: Wednesday, September 06, 2017 10:07
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cortical Parcellation Yeo2011
Hi list,
I have already run by recon-all -all all my subjects in order to run PetSurfer.
Output stats is saved in gtm.stats.dat and values correspond to
Desikan-Killiany Atlas, However, I am interested in calculating values using
Yeo atlas of 7 networks.
Do you have any suggestions to get Partial Volume Corrected values from Yeo
atlas for each subject?
Do I have to switch to Yao atlas during recon-all -all process or during gtmseg?
Thank you
Lorenzo
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