Hi Martin, Sorry for the slow reply. Antonin is right about the mri_segstats.
To map the surface parcellation from fsaverage to your individual subject's anatomical space, you can do the following: # 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 Regards, Thomas On Sat, Feb 11, 2017 at 5:01 AM, Antonin Skoch <a...@ikem.cz> wrote: > Dear Martin, > > I think that this thread is relevant for you: > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34508.html > > You would have to map Yeo atlas to individual brain and then extract the LGI > values using command: > > mri_segstats --annot my_subject_id lh aparc --i > $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > where aparc replace by name of your generated Yeo atlas annot file. > > Regards, > > Antonin Skoch > > > Hi everyone, > > I was wondering if someone could please address the following question > regarding FreeSurfer usage. > > I would really appreciate any help. > > Thanks. > > Hi, > > I used following command to extract LGI values from a set of subjects: > > recon-all -s <subj> -localGI > > Output stats is saved in lh.aparc_lgi.stats file. By default, its > calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am > interested in calculating LGI values using Yeo atlas of 7 networks. I was > wondering how can I change the default atlas to Yeo atlas to get LGI value > for each subject. > > Thanks a lot. > > > _______________________________________________ > 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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
