I ran fmriprep (1.0.3) and some of the output data has poor/errors in skull-stripping (I think this is potentially due to issues with contrast in the image). I wondered if there was a way to try to troubleshoot this effectively (trying to use another skull strip template? Or if I could adjust the skull-stripping threshold via the docker command line?).
Another run from the same subject processed fine (run2 pngs)–
So I was unsure how best to proceed? Are there reasonable ways to reprocess the first run or should I simply exclude it? Any advice or thoughts are greatly appreciated!