Thanks, Alfonso!
 
I was using the "manually defined" option for the slice-acquisition order. It seems that I ran preprocessing twice on the same subject by accident and this caused the slice order to not match the total number of slices in the functional image. 

I re-ran the default preprocessing pipeline on the raw data, and that worked great . Also, the slurm submission is working fine after setting the MCRROOT definition. Thanks, again! 

Best regards,
Jake