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More broadly, the outputs of fMRIPrep conform to the BIDS-Derivatives specification, Release Candidate 1. When fMRIPrep has completed running, the output directory looks like this.Ī detailed description of the fMRIPrep outputs can be found here.
For simplicity, we recommend placing the input, output and analysis levels prior to any options.įmriprep-docker /Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/Nifti /Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/derivatives participant -participant-label 2475376 -fs-license-file /Users/franklinfeingold/freesurfer.txt -ignore slicetiming You may pass additional arguments as you would to fMRIPrep. Please note that the ‘sub-’ prefix is not included. Lastly, we provide the participant label tag to indicate which participant to run. Followed by passing the keyword ‘participant’ as the third argument, which selects the analysis level that will be executed (see the BIDS-Apps specification for further details and possible values in the case of fMRIPrep, only ‘participant’ is available). The next part is providing the output directory. To break down the command: the first argument is providing the input path to the BIDS dataset. The command to execute it is illustrated below. More information regarding this can be found here.
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We saved our license into a file called /Users/franklinfeingold/freesurfer.txt. Please save this license file to your computer.
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After filling out the registration form, a license file will be sent to the email provided. To get the license and run FreeSurfer, FreeSurfer requires users to register for free, here. Because of this, fMRIPrep requires a FreeSurfer license.
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.
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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.
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