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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