Re: [Freesurfer] pwd: permission denied

2012-03-07 Thread Marcel Zwiers
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 exec

Re: [Freesurfer] pwd: permission denied

2012-03-07 Thread Marcel Zwiers
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 exec

Re: [Freesurfer] pwd: permission denied

2012-03-07 Thread lordowen
Hi Marcel: Do you using Mac? If so, please unlock your "root" account, then change to the root account (re-login as root or using 'su' command in terminal window). We also have this problem one month ago. It is because that the default setting for root account in OS X 10.7.x is hidden in the begin

Re: [Freesurfer] pwd: permission denied

2012-03-06 Thread Marcel Zwiers
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/Freesurfe

[Freesurfer] pwd: permission denied

2012-03-05 Thread Marcel Zwiers
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