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
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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!
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!
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