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