Hi Annie, mri_surf2surf is complaining that it cannot write out the annotation.
Just to clarify, is your subject called test_run_allindex? In other words, is the variable s equal to test_run_allindex? Does the directory "/home/annie/test_run_allindex/label/" exist? If not, then you first need to create the directory first, and then mri_surf2surf can write the resulting annotation file into the directory. Cheers, Thomas On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 <poohann1...@gmail.com> wrote: > Hi Professor Yeo : > > We tried the code >>> 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 > However there came an error of "could not write annot file > /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot > No such file or directory" > And we checked our individual subject's label there isn't > lh.Yeo2011_7Networks_N1000.annot > Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into our > subjects/label first? > What can we do ? > Thank you very much! > > Best wishes, > Annie > > > 2015-05-05 8:36 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>: > >> Hi Annie, >> >> Please cc the freesurfer list when you reply because there might be >> other people more qualified to answer your question. >> >> Based on what you are saying, I think you can first use mri_surf2surf >> (with the "sval-annot" flag) to transform the 2011 functional networks >> .annot file from fsaverage space to the subject's native surface >> space. Type "mri_surf2surf --help" to see examples. >> >> You can then use mris_anatomical_stats to compute thickness statistics. >> >> Cheers, >> Thomas >> >> On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 <poohann1...@gmail.com> wrote: >> > Dear Pro. Yeo: >> > >> > Very appreciate for your reply ! >> > >> > We are trying to use your definition of the functional network regions >> > to >> > re-parcellate our images >> > and get the regions of volume or cortical thickness for our study >> > interest >> > of structural network. >> > However, we did not want to re-run the first recon-all again due to it's >> > spending to much time. >> > And we are still can't find the way to solve this problem. >> > Thank you very much for helping us! >> > >> > Best wishes, >> > Annie Chen >> > >> > 2015-05-02 8:25 GMT+08:00 Thomas Yeo <ytho...@csail.mit.edu>: >> >> >> >> Hi Yu-Chieh, >> >> >> >> I am cc-ing the freesurfer list who may help you with your issues. >> >> >> >> Can you explain what exactly you are trying do? The parcellation is >> >> released in different resolutions including fsaverage5. Why can't you >> >> just use the fsaverage5 parcellation? >> >> >> >> Cheers, >> >> Thomas >> >> >> >> On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 <poohann1...@gmail.com> wrote: >> >> > Dear professor Yeo : >> >> > >> >> > My name is Yu-chieh Chen , I am a graduated student from National >> >> > Taiwan >> >> > University of medical school, and my supervisor is professor Susan >> >> > Shur-Fen >> >> > Gau from department of psychiatry, National Taiwan University >> >> > Hospital & >> >> > College of Medicine. We are very interesting about your paper >> >> > published >> >> > in >> >> > 2011 which using resting MRI to separate brain regions to functional >> >> > networks. We'd like to use your percellation to re-separate the brain >> >> > regions based on your released data in Freesurfer( >> >> > http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). >> >> > And >> >> > use >> >> > these volume of brain regions for our study, however, there comes the >> >> > problem that we assumed that we can change the fsaverage into >> >> > fsaverage5, >> >> > thus we may get the new volume of the parcellation_Yeo. But it is not >> >> > work. >> >> > So I send this email for help. Last , I am very appreciate your >> >> > kindness >> >> > and >> >> > very sorry for my inappropriate and rough. >> >> > Thank you very much for read this email and sorry for occupied your >> >> > time. >> >> > >> >> > Best wishes, >> >> > Yu-chieh Chen >> >> > >> > >> > > > _______________________________________________ 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.
