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 <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FW: problem with hard coded directory
(/scratch)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <568abbfc.5000...@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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