Hi Markus,

Thank you for this, yes I am running Mac OS 10.9.2, and the freesurfer command freeview loads the data fine when I start up matlab from the bash terminal (even without using XQuartz, my equivalent of X11) and call this command. Thanks for the quick help! Barbara

On Tue, Sep 9, 2014 at 12:59 PM, Markus Gschwind markus.gschwind@gmail.com wrote:

Hi Barbara,

You haven't told us which OS you use. For example in Mac OS it is necessary to start up MATLAB by typing matlab into the X11 terminal, otherwise the system OS will not recognize the commands given via matlab (e.g. system('mycommand') .)

Best, Markus

2014-09-09 13:45 GMT+02:00 Barbara Kreilkamp bakk.hbg@googlemail.com:

...

Dear Freesurfers,

Is there a way of calling freesurfer-scripts from within MATLAB? I know there are some setups needed to make MATLAB understand where it can find the commands (I have done this before with FSL). I am using bash, and when I type the Freesurfer commands in a terminal by hand, they work. So I am guessing it must have to do with setting up the environment:

freesurf_path ='Applications/freesurfer'; setenv('FREESURFDIR',freesurf_path)

setenv('FREESURFOUTPUTTYPE','NIFTI_GZ') curpath = getenv('PATH'); setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath));

Thanks a lot for any help, Barbara

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