FSL Bet Tool- not working

Hi there,

I have recently updated from FSL 5.0 to 6.0 and the bet tool is no longer working for diffusion data. The image file is created, however, only the first b0 image has the skull removed. This is the case even when trying to reprocess subjects that were processed on FSL 5.0. Has anyone experienced this same issue or have any solutions?


fMRIPrep can’t upgrade FSL to 6.0 for this issue, so it is real. Unfortunately, I don’t know enough to say anything else.

Maybe @Fidel could illuminate us?


Jennifer asked the same question in FSL’s mailing list and Paul McCarthy answered this: