Hi Annie, I assume this means 5202 is your subject ID? Maybe you should check if /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot exist?
If so, you can run mris_anatomical_stats to generate statistics for the parcellation. Cheers, Thomas On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 <poohann1...@gmail.com> wrote: > Hi Professor Yeo : > After I rechecked the directory and run again mri_surf2surf > I got the result: > "Saving target data > Converting to target annot > Saving to target annot > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot" > The file of 5202/label didn't come out with lh.Yeo2011_7Networks_N1000.annot > But it seems succeed, right? > How can I get the stat of this parcellation ? > > Thank you very much! > > Best wishes, > Annie > > 2015-05-12 6:06 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>: > >> 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.
