afni.nimh.nih.gov

I've had a few problems with MATLAB resetting the library path. As a fix, I've appending the following to all AFNI commands before calling them via MATLAB. Hope this helps!

export DYLD_LIBRARY_PATH=""

So for example a command to do quick masking of a dataset via 3dcalc looks like this:

mask_command = ['export DYLD_LIBRARY_PATH=""; 3dcalc  -a ',...
                           reg_outputfile, '.TMP+tlrc -b mask.nii.gz ',...
                           '-expr ''step(b)*a'' -prefix ', reg_outputfile];

system(mask_command);