Gari,
Hi, your situation seems odd. Freesurfer does not require anything special in terms of a file system, or modify system settings of any sort, so I'm not sure what is happening in your situation. The recon-all script does set 'umask 002', which clears the write-bit for 'other' users. Perhaps this is conflicting with some special system setting? although i have never heard of a problem with umask so i'm grasping at straws here. sorry!
Nick
Thanks for the answers. I am not the sys admin, but I think I can answer both questions:
I assume the system is in read-write mode since the rest of the programs
(i.e. Matlab) are working.
The SUBJECT_DIR is in each personal space, I mean:
--- FS is installed in a Linux CentOS 5 machine, I have an account in that machine (and I can work normally if my SUBJECTS_DIR is in that machine) --- I have a personal drive space in the NFS 4, and I used to have my SUBJECTS_DIR in that drive, but after they upgraded it to NFS 4, it didn't work again.
We have a new cluster now, they are testing it, it has Red Hat installed,
with FS 5.2, and I've been told that it cannot write (same problem).
The strange thing is that other programs work fine with this setup.
Do you think the problem is in the file system config (it seems so) or in FS config to be able to work with NFS 4?
I have asked the sys admin for the output of the system-config-nfs, I don't have admin privileges to run it.
thanks again! Gari
On Fri, May 10, 2013 at 11:46 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Gari,
At the NMR Center we use NFS v4 without problems with freesurfer. Is the SUBJECTS_DIR writable? Note that in the default freesurfer distribution, the freesurfer/subjects directory is not writable (contains sample and template subjects).
Nick
Hi, Has anybody got problems using FS with NFS v4? We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system.
Many thanks, Gari
---------- Forwarded message ---------- From: Garikoitz Lerma-Usabiaga garikoitz@gmail.com Date: Tue, May 7, 2013 at 5:25 PM Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2 To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Hi FS experts, we have changed our file systems to NFS v4 and we found that FS cannot write to it (I mean, FS installed in an app server and subjects in the file system is not working). Last new I have is that FS in CentOS could read but not write and in
Red
Hat could not write or read.
Is it a known problem? Is it something going on with FS or the problem
is
in our end? (the rest of the programs are working fine: FSL,
Matlab...)
Many thanks, Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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