Message: 8
Date: Mon, 16 Nov 2015 12:52:20 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Advice for FreeSurfer developers
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <564A17D4.6090707@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Do you know what command was looking for matlab?

On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote:

Hi Doug,

I used mostly the default options, nothing special:

recon-all -autorecon1 -clean-tal -expert my_options.txt -hires

where the file my_options.txt contains some options for nu_correct.
Then I entered

recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires

The error occurred with the last recon-all command.
BTW, I really don't know if the -clean-tal option is needed with FS v6.

Cheers
Ed


On 11 Nov 2015, at 18:00, <freesurfer-request@nmr.mgh.harvard.edu
<mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote:

Message: 9
Date: Wed, 11 Nov 2015 11:08:46 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Advice for FreeSurfer developers
To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5643680E.1030800@nmr.mgh.harvard.edu
<mailto:5643680E.1030800@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Ed, generally recon-all does not need matlab. Are you running the
gyrification analysis? That should be the only thing that needs matlab.
doug

On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote:

Dear developers,

Is it possible to check the presence of Matlab runtime right at the
start of recon-all
in FreeSurfer v6 instead of a long way down in the pipeline. After
36 hours for
a high-res data processing I got this unexpected error message.
Thanks in advance.

Cheers
Ed
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