Do you have the problem if you do not include the hippo subfields?
On 01/07/2016 08:15 AM, Fengji Geng wrote:
Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know.
we ran recon-all -all -s <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch.
I can also send you the strace output if needed.
Thank you!
Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 568ABBFC.5000702@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
Can you give us specific examples of problem programs?
On 01/04/2016 09:54 AM, Fengji Geng wrote:
Hello Bruce,
Happy New Year!
After we reported the error related to '/scratch' several weeks ago (see the email attached below), we tested the newest version of freesurfer 6.0 recently, it looks likes that a lot of "if (-e /scratch)" have been changed to "if (-dw /scratch)". However, there are still a lot of binaries in the bin directory that match the string "scratch", which cause the same error that I encountered before. I am wondering if it is possible for you to fix '/scratch' in the bin directory.
Thank you!
Fengji
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