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...@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 notwork for 30 subjects. I then went to
investigate one by one and I amgetting a Permission denied error for some
reason. I confirm thatrecon-all has been performed and also that I have
read/write/executepermissions. See below for the log. Any ideas why this
could behappening 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
--tvalSPN01_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
fileSPN01_CMH_0079_01/label/lh.500_sym.aparc.annot___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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