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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lorenzo Pini [pini.lorenzo2@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