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Directory Structure
To comply with both BIDS specification and Snakemake standard, the following directory structure has been adopted (with example intermediate workflows):
results/ <-- list of derivative datasets
fmriprep
dataset_description.json
sub-01/
sub-02/
hippunfold
sub-01
work
The top-level directory retains a single results
folder containing all of the processed data. This results
folder contains the final output (eg. necessary files) of the workflow and stores them according to the BIDS standard. To comply with the standard, a dataset_description.json
file is also included in this results folder.
sourcedata
contains the intermediate files generated to produce the final output. The directory is named to comply with the BIDS standard, while also being ignored by the BIDS validator. Each sub-directory within this directory is associated with a .smk
file, with individual subject directories nested within the sub-directories.