External Email - Use Caution       

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:
>
>
>         External Email - Use Caution       
>
> 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
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--
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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