You should be able to use the 5.3 version. Regards, Thomas
On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs <b.ov...@neura.edu.au> wrote: > Hi Thomas, > > Thanks for your reply. > > The fsaverage directory I have for fs v 5.1 does not include the lh and rh > Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of > fsaverage. Can I still use the 5.3 version annot files or would I need a > seperate set processed with version 5.1? > > Kind regards, > > Bronwyn Overs > Research Assistant > [image: Neuroscience Research Australia] > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > *M* 0411 308 769 *T* +61 2 9399 1883 > neura.edu.au > > [image: Follow @neuraustralia on twitter] > <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook] > <https://www.facebook.com/NeuroscienceResearchAustralia>[image: Subscribe > to the NeuRA Magazine] <http://www.neura.edu.au/help-research/subscribe> > On 23/06/2016 3:17 pm, Thomas Yeo wrote: > > Hi Bronwyn, > > You raise a good point. You can consider creating a cortical mask using > aparc+aseg.mgz and use that to mask the networks. > > However, another approach (which might be more accurate) is to take > cortical networks in fsaverage space and transform to your subject's > surface and then transform into your subject's volume: > > # Transform from fsaverage to subject's surface > >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh > --sval-annot *lh.Yeo2011_17Networks_N1000.annot* --tval > $SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot* > > # Transform from subject's surface into your subject's volume (I am not > super sure about this. You probably want to double check the output is > correct) > >> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o > outfile.nii.gz --hemi lh --subject HS_001 **--regheader* > > --Thomas > > On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs <b.ov...@neura.edu.au> > wrote: > >> Hi Mailing List, >> >> I am attempting to apply the Yeo 2011 7-network fucntional parcellations >> to a set of fs MRIs processed with v5.1.0. Below are listed the first three >> steps I plan to take and I am seeking advice as to: >> >> A) Whether this approach is valid. >> B) Steps to take next. >> >> >> >> * Steps 1-3: * >> >> *1. Run MNI152 1mm template through recon-all* >> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid >> Yeo2011_MNI152_FS >> recon-all -all -subjid Yeo2011_MNI152_FS >> >> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* >> mri_vol2vol --mov >> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s >> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z >> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest >> >> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* >> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ >> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz >> --nearest --inv-morph >> >> >> When previously mapping the Choi 2012 straital parcellations, steps 4 and >> 5 were: >> >> 4. *Creating a striatal mask in the native subject's space from >> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens >> (26 & 58)*: >> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match >> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz >> >> *5. **Using this mask to mask the choi striatal parcellations* >> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz >> Yeo_atlas_subjID_mask.nii.gz >> >> >> Do I need to do a similar thing for the Yeo cortical parcellations and if >> so what regions should I include in the cortical mask? >> -- >> >> Kind regards, >> >> Bronwyn Overs >> Research Assistant >> [image: Neuroscience Research Australia] >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> *M* 0411 308 769 *T* +61 2 9399 1883 <%2B61%202%209399%201883> >> neura.edu.au >> >> [image: Follow @neuraustralia on twitter] >> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook] >> <https://www.facebook.com/NeuroscienceResearchAustralia>[image: >> Subscribe to the NeuRA Magazine] >> <http://www.neura.edu.au/help-research/subscribe> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. 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