Hallelujah ! Problem solved! Here's what happened: both tcsh pwd and /bin/pwd
give errors when a directory is executable (+x) but not readable (-r). And in
my case, the colleague of mine fully opened up $SUBJECTS_DIR for me, but (and
this is also how it should be done) only provided me with executable rights for
the parent directories. I haven't figured out why recon-all needs to call pwd
on these parent directories at all -- I leave that one for the recon-all tcsh
gurus :-) My hack was to replace every pwd call in the recon-all script by the
built-in bash pwd call (which only needs +x permissions). It's not very pretty,
but hey, must of us aren't! To be precise, this is what did it for me (NB: some
of the pwd replacements may be unnecessary): diff myrecon-all
/opt/freesurfer/bin/recon-all 296c296 < set PWD = "bash -c 'pwd'"; --- > set
PWD = pwd; 298c298 < # if ( -e /bin/pwd ) set PWD = /bin/pwd --- > if ( -e
/bin/pwd ) set PWD = /bin/pwd 361c361 < set freesurfer_home_true = `$PWD`; ---
> set freesurfer_home_true = `pwd`; 382c382 < $PWD >> $ENVF --- > pwd >> $ENVF
3819c3819 < echo "PWD `$PWD`" >> $ErrorFile --- > echo "PWD `pwd`" >>
$ErrorFile 3880c3880 < set InVolDir = `$PWD`; --- > set InVolDir = `pwd`;
4943c4943 < setenv FREESURFER_HOME `$PWD`; --- > setenv FREESURFER_HOME `pwd`;
Hope this may be of use to anyone encountering the same problem and that this
tcsh bin & /bin/pwd problem may be taken into account in future recon-all
versions. All the best and thanks a lot for all your time and kind help,
Marcel. > >> 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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