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

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