Hi Stefano, Here's what you can do. In your shell (assuming you are using c shell)
# First set variable s to be subject id >> set s = 100306_QD95CU_FS # set freesurfer environmental variable SUBJECTS_DIR to point to where the data is >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/ # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage # use "-sval-annot" option to transfer annotation >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval-annot >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot # use "sval" option to transfer confidence map. >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz Cheers, Thomas On Sun, Jul 20, 2014 at 10:33 PM, <std...@virgilio.it> wrote: > Hi list and Thomas, > > I'm running the first step to use Yeo's parcellation. The running is wrong. > > mri_surf2surf --s Control01 --hemi lh --sval-tal-xyz white --tval > lh.white.Control01 --tval-xyz --trgsubject > fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz > > Reading target surface reg > $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg > MRISread( > $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg): > could not open file > Not a directory > mri_surf2surf: could not read surface > $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ytho...@csail.mit.edu > Data: 7-feb-2014 9.49 > A: <std...@virgilio.it> > Cc: "freesurfer"<freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Yeo parcellation > > Hi Stefano, > > A) From FreeSurfer 5.2 onwards, the Yeo parcellation files can be > found inside $FREESURFER_HOME/subjects/fsaverage/label/, so you can > simply use those files there instead of downloading from the wiki. > > B) You can use mri_surf2surf to transform the annot files from the > fsaverage "subject" to the individual subjects' surface. There is an > example of how to do it if you run "mri_surf2surf --help" > > C) Once you have created the subject's specific annot file from part > B, I believe you must first run mris_anatomical_stats, and then run > aparcstats2table. However, I am not sure about this, so someone on the > list should correct me if I am wrong! > > Regards, > Thomas > > On Fri, Feb 7, 2014 at 3:58 PM, <std...@virgilio.it> wrote: >> Hi list, >> >> I have download the files of Yeo parcellation from >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip. >> >> I have two questions, please. >> >> A- Which is the directory where I should put these files? >> B-I have already run by recon-all -all all my subjects. How can I added to >> them Yeo parcellation? >> C-I'd like also calculate the cortical thickness for each Yeo's ROI. Is >> possible with aparcstats2table? >> >> Thanks. >> >> Regards, >> >> >> Stefano >> >> _______________________________________________ >> 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 > > > > _______________________________________________ > 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
