It looks like the FSL paths didn't get transferred to matlab, which I've seen a few times before.  One workaround for this is to go into the matlab code (i.e., METAlab_GTG_preprocess.m) and put the whole path for mcflirt (i.e., on line 1301, replace !mcflirt with !/usr/local/fsl/bin/mcflirt or whatever the path is).  Hopefully that will work....