I updated the mcflirt path, but now was having other fsl configuration issues. Matlab output below. 

>> METAlab_GTG
Warning: matlabpool will be removed in a future release.
To query the size of an already started parallel pool, query the 'NumWorkers' property of the pool.
To check if a pool is already started use 'isempty(gcp('nocreate'))'.
ERROR:: Environment variable FSLOUTPUTTYPE is not set!
Please make sure that the appropriate configuration file is sourced by your shell (e.g. by putting it in .profile).
e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh"
e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh"
Error using checkfilename>validateFilename (line 165)
Function GUNZIP was unable to find file
''/Users/jamielarshanson/Desktop/GIMME_test/2011031012402_rest_mcf.nii.gz''.

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I then updated METAlab_GTG_preprocess_GUI to include those fsl files (edits below), but it didn't seem to work/didn't fix the issue (edits below). Any other thoughts? Thanks again for the help!


if subfunc_out.MC == 1
eval(['! . /Users/jamielarshanson/Research/Software/fsl/fsl/etc/fslconf/fsl.sh ']);
eval(['!export FSLOUTPUTTYPE=NIFTI_GZ']);
eval(['!/Users/jamielarshanson/Research/Software/fsl/fsl/bin/mcflirt -in ',orig_func_filename,' -plots']);
orig_func_filename = strrep(orig_func_filename,'.nii','_mcf.nii');
par_filename = strrep(orig_func_filename,img_ext,'.par');
end