External Email - Use Caution
Hello Ellen, I suspect that you really do not have the system privileges to read/write every subject directory. I have run into this with other commands that scan multiple subject directories. Assuming there is one top level directory that contains all the subject directories, and it’s OK for you to try and set/change permissions on those files, then in terminal window you could “cd” to that parent directory,
$ cd <path to top of tree containing all subject subdirectories> - and then try running the following command, $ find . -maxdepth 1 -type d -exec chmod 755 {} ; -print That will try and change the permissions of every subdirectory there such that you can read and write to it. But if you don’t have permission to access some of those directories, then you will get an error.. You may have to find someone wit, e.g., admin/root. privileges to change the permissions on the subdirectories the chmod command fails on.
- R. On Sep 9, 2020, at 03:19, Ellen Ji <ellen.ji@bli.uzh.ch> wrote: External Email - Use Caution Dear experts,I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied error for some reason. I confirm that recon-all has been performed and also that I have read/write/execute permissions. See below for the log. Any ideas why this could be happening to specific subjects? mri_surf2surf --srcsubject fsaverage_sym --trgsubject SPN01_CMH_0079_01 --hemi lh --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annotSetting mapmethod to nnf7.1.0setenv SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0cd /home/eji/projects/spins/preproc/freesurfer/subjects/w0mri_surf2surf --srcsubject fsaverage_sym --trgsubject SPN01_CMH_0079_01 --hemi lh --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annotsysname Linuxhostname nu2machine x86_64user ejisrcsubject = fsaverage_symsrcval = (null)srctype =trgsubject = SPN01_CMH_0079_01trgval = SPN01_CMH_0079_01/label/lh.500_sym.aparc.annottrgtype =srcsurfreg = sphere.regtrgsurfreg = sphere.regsrchemi = lhtrghemi = lhframe = 0fwhm-in = 0fwhm-out = 0label-src = (null)label-trg = (null)OKToRevFaceOrder = 1UseDualHemi = 0Reading source surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.sphere.regLoading source dataReading surface file /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.origreading colortable from annotation file...colortable with 161 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)Reading target surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0079_01/surf/lh.sphere.regDoneUsing surf2surf_nnfr()Mapping Source Volume onto Source Subject Surfacesurf2surf_nnfr: building source hash (res=16).Surf2Surf: Forward Loop (123600)Surf2Surf: Dividing by number of hits (123600)INFO: nSrcLost = 61776nTrg121 = 123600, nTrgMulti = 0, MnTrgMultiHits = 0nSrc121 = 85136, nSrcLost = 61776, nSrcMulti = 78706, MnSrcMultiHits = 0.488705Saving target dataConverting to target annotSaving to target annot SPN01_CMH_0079_01/label/lh.500_sym.aparc.annoterror: Permission deniederror: could not write annot file SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B