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.gschw...@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....@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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