Hi Chris,

Something is going wrong in the script that reads in the out-of-plane motion parameters from the text files stored in _pestica/empslmoco_volslc_alg_vol_ directory.  FYI, those names were poorly chosen, I did not intend them to be as long as possible.

I think your error is occuring when this command is called:

mocoparams=read_motion_newslicealg('tempslmoco_volslc_alg_vol_$epi.slicemocoxy_afni/motion.wholevol_zt');


The shell script also echoes out the matlab command to be run, right before calling matlab. Can you check the tempslmoco_volslc_XXX directory inside _pestica/? There should be zdim number of files in it (the number of slices).

Erik