So I'm new to fmriprep, and it seems like an incredibly useful tool, but something appears to have gone wrong in the ANTS brain extraction. If I were running each of the composite tools by hand, I could tweak the thresholds for the brain extraction until it looked right, but how do you do something like this with fmriprep?
Report view below:
fmriprep --participant_label pixar001 --output-space template --no-freesurfer -w work BIDS test_fmriprep participant
using singularity 2.3 with
singularity shell docker://poldracklab/fmriprep:latest