The fmriprep workflow takes as principal input the path of the dataset that is to be processed. The only requirement to the input dataset is that it has a valid BIDS (Brain Imaging Data Structure) format. This can be easily checked online using the BIDS Validator.
The exact command to run fmriprep depends on the Installation method. The common parts of the command follow the BIDS-Apps definition. Example: :
fmriprep data/bids_root/ out/ participant -w work/Logs and crashfiles are outputted into the <output dir>/logs directory. Information on how to customize and understand these files can be found on the nipype debugging page.
The documentation of this project is found here: http://fmriprep.readthedocs.org/en/latest/.
If you have a problem or would like to ask a question about how to use fmriprep, please submit a question to NeuroStars.org with an fmriprep tag. NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
All previous fmriprep questions are available here: http://neurostars.org/tags/fmriprep/
To participate in the fmriprep development-related discussions please use the following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging Please add [fmriprep] to the subject line when posting on the mailing list.
All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/fmriprep/issues.