Hi Fengji, Sorry for the late reply; I was on vacation and totally missed your question. The hippocampal subfield module uses /scratch to create temporary files if available. If not, it creates a directory under the tmp directory inside the subject directory. It was coded this way because in our system, because of the way the cluster is setup, writing to /scratch is way more efficient. For now, the only thing you can do is to enable writing permissions on /scratch, or deleting /scratch. For the future: maybe we should remove the /scratch check and go to the subject's tmp directory directly (Zeke, Nick, what do you think?) Cheers, Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
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From: "Fengji Geng" gengf@umd.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, January 14, 2016 7:46:44 PM Subject: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)
Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you!
----- Fengji
From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch)
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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