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