Hi Michael, Thanks for your help and suggestions! > I'd have to try to recreate
the error, but I have an idea of what it
> could be (assuming
> /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness/BIG1026_1
> is a directory).
Actually not yet,
/home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness is a directory
but BIG1026_1 is supposed to be created by recon-all (but wasn't as a
consequence of the error). > While you may have read, write, and execute
permissions to your
> colleague's directory, you must make sure that these permissions have
> been recursively added to the contents of that directory (child
> directories, child directory files, and directory files).
There are only *.nii.gz files in that directory plus a few extra files and
(symbolic links to) folders that I assume should have nothing to do with the
error? The content looks like this (ls -al): drwxrwxr-x 2 marhoo big 352256 Mar
6 09:51 ./ drwxrwx--x 15 marhoo big 4096 Feb 29 15:49 ../ -rw------- 1 marzwi
big 12219623 Mar 2 16:06 BIG1026_1.nii.gz [..] -rw------- 1 marzwi big 12219623
Mar 2 16:06 BIG4025_1.nii.gz -rw-rwxr-- 1 marhoo big 75806 Feb 27 10:54
BIG_aseg_stats.log* lrwxrwxrwx 1 marhoo big 34 Feb 19 09:12 fsaverage ->
/opt/freesurfer/subjects/fsaverage/ lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12
lh.EC_average -> /opt/freesurfer/subjects/lh.EC_average/ lrwxrwxrwx 1 marhoo
big 38 Feb 19 09:12 rh.EC_average -> /opt/freesurfer/subjects/rh.EC_average/
-rw-rwxr-- 1 marhoo big 18200 Sep 27 10:39 v5.0.txt* -rw-rwxr-- 1 marhoo big
3220 Sep 27 10:39 v5.1.txt* -rw-rwxrw- 1 marhoo big 523 Feb 24 10:07
.xdebug_tkmedit* > I believe that your problem is that the file BIG1026_1.nii.gz
> (however, from my experience this file should not simply be in the
> BIG1026_1 folder but in the orig directory of the mri folder) has not
> inherited the specified permissions from its parent directory.
My username is marzwi, I am member of the big group and I have rw permissions
of all the files and directories (see listing above) . > If this does not
correct the error, set the environmental SUBJECTS_DIR
> variable to the directory housing the subject directories (making sure
> that your colleague gives you sufficient access to this directory),
> lose the -sd path in the command, and make sure that you have read,
> write, execute permissions recursively added to the directories and
> files that you will be working with.
I did that but the error message remains. Here's the full message, started from
a newly opened bash terminal: --------
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up
environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer
FSFAST_HOME /opt/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR
/opt/freesurfer/subjects MNI_DIR /opt/freesurfer/mni FSL_DIR /opt/fsl
mentat002:$ export
SUBJECTS_DIR=/home/mrphys/marzwi/BIG/Freesurfer_CorticalThickness mentat002:$
recon-all -subject BIG1026_1 -i BIG1026_1.nii.gz -autorecon1 /bin/pwd: cannot
open directory `../..': Permission denied mkdir: cannot create directory
`/BIG1026_1': Permission denied mkdir: cannot create directory `/BIG1026_1':
Permission denied cp: cannot create regular file
`/BIG1026_1/scripts/build-stamp.txt': No such file or directory cat:
/BIG1026_1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer
build stamps do not match Subject Stamp: Current Stamp:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is Actual
FREESURFER_HOME /opt/freesurfer-v5.1 /BIG1026_1: No such file or directory. >
Another option would be if your colleague set up a "subjects
> directory" within his parent directory and add each subject's folder
> to this directory and then setting this as your SUBJECTS_DIR variable
> (ensuring you have read, write, execute permissions).
I created a subfolder, copied the BIG1026_1.nii.gz file into it and ran
recon-all using this subfolder as SUBJECTS_DIR but I kept getting permission
denied errors. > I hope this helps; however, not knowing the version of free
surfer
> that you are running nor the operating system makes it difficult to
> trou bleshoot your problem. Let me know if you arrive at a solution or
> require further assistance.
> Thanks,
> Michael Nowak
I hope the info above can help troubleshooting my problem. Thanks a lot
Michael! Cheers, Marcel On Mon, Mar 5, 2012 at 9:55 PM, Marcel Zwiers <
m.zwi...@fcdonders.ru.nl > wrote: > Hi, > > I am new to FS and have encountered
a weird problem that I do not know how to solve and did not find any earlier >
postings on. When I run recon-all on a file in my own home directory everything
works normally: > > recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test
-i BIG1026_1.nii.gz > -autorecon1 > [..] > > However, if I run the same command
on the same file, except that this file is now located in a directory of a >
colleague of mine that I certainly have full access to (+r+w+x), I immediately
get a 'permission denied' error: > recon-all -subject BIG1026_1 -sd
/home/control/marhoo/Projects > /BIG/Freesurfer_CorticalThickness -i
BIG1026_1.nii.gz -autorecon1 > pwd: cannot open directory `../..': Permission
denied > /bin/pwd: cannot open directory `../..': Permission denied > mkdir:
cannot create directory `/BIG1026_1': Permission denied > [..] > > From the
error message it seems to me as if FS is trying to access the parent directory
(of which I do not have > full rights but only -r-w+x)? As this does not make a
lot of sense to me I suspect there must be another cause > and hope you have
any ideas here. > > Cheers, > Marcel -- Marcel Zwiers www.ru.nl/donders MR
techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and
Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The
Netherlands
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