Mostly, running shell commands in Matlab works fine, and little has to be specific for AFNI programs to work. Matlab uses the sh shell (neither bash nor tcsh, but the Bourne shell), and the configuration for that shell needs to be correct. You can either have Matlab use a different shell through environment variables like MATLAB_SHELL or add PATH and DYLD_LIBRARY_PATH to a .profile file in your home directory. On a Mac, you may also need to set DYLD_LIBRARY_PATH in the terminal or shell used to start MATLAB and launch from the command line rather than run it from a GUI launcher. Security protection implemented on the MacOS could be turned off too. See these links for some more info.
[
www.mathworks.com]
[
osr600doc.xinuos.com]
[
www.mathworks.com]
[
afni.nimh.nih.gov]
