fMRIPrep uses FreeSurfer to reconstruct anatomical surfaces of the brain as well as some registration steps. )ģ) Please be cautious running multiple subjects in parallel due to space and memory limits on your machine. NOTE: Please observe there are a few BIDS validator warnings that may need to be attended to before running fMRIPrep.ġ) To do the susceptibility distortion correction, the IntendedFor metadata keys need to be defined for every field map that is to be applied.Ģ) To do the slice timing correction, the slice timings need to be defined in the BOLD json metadata file (if you want to ignore the slice timing correction, please add the ‐‐ignore slicetiming option, the command to do this is shown below. Please find pictured below our BIDS validated dataset. We will only be taking sub-2475376 session 1 anatomical and resting state scan at TR=1400ms. Pip install -user -upgrade fmriprep-dockerįor this tutorial, we will be using the Nathan Kline Institute (NKI) Rockland Sample – Multiband Imaging Test-Retest Pilot Dataset.
