I’m not 100% sure it ran to completion. I checked my jobs and one is still running, but I submitted other jobs around that same time that should have taken much longer than this job so I don’t think it’s this. I have an error and output file. The error file only mentions that the root directory I set for my preprocessing output is not “valid”, but the other outputs are in that directory. I ran fmriprep on a different set of data and it worked perfectly, but this dataset did not give me that confounds file for run 2.