Re: [Freesurfer] Run recon-all in MATLAB

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Hi Tim,

Thanks a lot for the quick response. I used system and it is working now 🙂

Have a nice day,

Aldo ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer ts+ml@rcmd.org Sent: Wednesday, August 26, 2020 1:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Run recon-all in MATLAB

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Hi Aldo,

What do you mean by 'still is not working'? What command did you run where (Matlab or Shell), and what was the error message?

I've had a quick look at that website, and from what I can tell it does not try to tell you how to run recon-all from Matlab. All it does is tell you how to get the FreeSurfer matlab functions (in $FREESURFER_HOME/matlab/) available in Matlab. E.g., after following that setup, you should be able to call 'read_curv()' from Matlab to read morphometry data files like <subject>/surf/lh.area.

If you want to run recon-all (or any other system command) from Matlab, have a look at the Matlab 'system' function. I would recommend against it though.

Best,

Tim

On August 26, 2020 at 7:10 PM "Camargo, Aldo" ACamargo@som.umaryland.edu wrote:

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Hi Freesurfer community,

Does someone know how to run recon-all on MATLAB ? I tried the settings suggest on https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/FreeSurfer, but still is not working;

Thanks a lot in advance and have a great day,

Aldo _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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