Hello Peter,

seems like more has changed

try this:

film_gls --rn=${nuisance_dir}/stats --noest --sa --ms=5 --in=${func_dir}/${rest}_pp.nii.gz --pd=${nuisance_dir}/nuisance.mat --thr=${minVal}


Furthermore we stopped support of the scripts as they are a reflection of the analyses as we did them in 2010. Now 4 years later standards have changed, e.g., we don't do global signal correction anymore, bandpass filtering is questioned etc. To accommodate these changes there is now C-PAC, which provides a full processing pipeline. You can find it here: http://fcp-indi.github.io/

Maarten