Skull-stripping for BOLD image (with variable contrast)



Hello all,

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?).

(run1 pngs)

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!

Thanks much!


This issue should’ve been fixed a few versions ago. Could you try the latest version (1.0.12)?


Are you able to share the first 50 volumes of the failing time series? We’re working towards building regression tests for that portion of the pipeline.


Yes, I shared it via DropBox (pardon my delay in sending it along). It’s linked here: