Fmriprep missing the confounds tsv for run




I used fmriprep to preprocess some data. I have 2 runs in this study. The job completed, but I’m missing the confounds tsv for run 2 in the directory.

My current output in my functional folder of the subject has all of these files


but there is no confounds tsv.

Does anyone have any suggestions?


Did it run to completion without errors? Could you share the HTML report?


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.


I noticed there was no html file so I reran the job and fmriprep worked this time. Strange since I didn’t change anything