Hi Ali, May I confirm that your data is T1 and not functional data? Here's what you can do to transfer the parcellation to your individual subject's surface mesh. After that you can use the usual commands to extract thickness, etc.
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 Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh <ali.radai...@hu.edu.jo> wrote: > Dear FreeSurfer experts, > > I have finished processing a group of brains MR images collected at 7T > scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine). > > However, we need to get the cortical parcellation based on functional > network connectivity. So I have downloaded the Atlas data > (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I have > few questions which I hope you will be able to help me on. > > 1- Do I need to repeat the "recon-all" process? > 2- If yes, how can I change the default Atlas that freesurfer uses? > 3- If no, what can I do to get the cortical parcellation based on finctional > networks from our processed data? > 4- At the end, shall I use the usual commands to extract the volumes, > thicknesses ...etc? > > > Many thanks for your help in advance. > > Ali > > > -- > Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radai...@hu.edu.jo > webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= > > > _______________________________________________ > 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
