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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.