Hi Doug,
Yes, I know. It’s the hippocampal subfields segmentation that needs matlab runtime.
Cheers, Ed
On 17 Nov 2015, at 18:00, freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 8 Date: Mon, 16 Nov 2015 12:52:20 -0500 From: Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <564A17D4.6090707@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To:freesurfer@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu/ mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <5643680E.1030800@nmr.mgh.harvard.edumailto: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 _______________________________________________ Freesurfer mailing list
This is a good point. We should run the check right away. Right now, the subfield module runs at the end, which means that everything else has completed just fine, but we should definitely check at the very beginning and say: "either download the runtime or remove the subfield flag"
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Gronenschild Ed (NP)" ed.gronenschild@maastrichtuniversity.nl To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, November 17, 2015 7:09:46 PM Subject: [Freesurfer] Advice for FreeSurfer developers
Hi Doug, Yes, I know. It’s the hippocampal subfields segmentation that needs matlab runtime.
Cheers, Ed
On 17 Nov 2015, at 18:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
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:
BQ_BEGIN 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:
BQ_BEGIN 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:
BQ_BEGIN 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 _______________________________________________ Freesurfer mailing list
BQ_END
BQ_END
BQ_END
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-
Eugenio Iglesias -
Gronenschild Ed (NP)