Converts HCP datasets into BIDS format. Works for both Lifespan and Young Adult.
lifespan.py: Converts Aging and Development (i.e. Lifespan) datasets to BIDS format.
hcpya.py: Converts Young Adult dataset to BIDS format.
python lifepsan.py --nda_dir <path to unprocessed data> --output_dir <path to output BIDS directory>
You can run python lifespan.py --help to see all options. The most important ones are:
- --nda_dir: Path to the unprocessed data directory. This should contain a directory titled 'imagingcollection01'.
- --output_dir: Path to the output BIDS directory. This directory will be created if it does not exist.
- --overwrite: If specified, will overwrite existing files in the output directory.
- --method: The method to use for linking/copying/moving the files. The options are "hardlink", "softlink", "copy", and "move". Default is "hardlink".
- --dry_run: If specified, will not actually copy/move/link any files, but will print out what it would do.
- --use_bids_uris: If specified, will use BIDS URIs instead of BIDS filenames in the JSON sidecar. URIs are the current standard, but as of April 2024 they were not supported by fMRIPrep.
I found it easiest to use the ndatools downloadcmd commandline tool to download the data. You can download downloadcmd using pip install nda-tools.
TODO: Add information about the HCP Young Adult dataset.
I was able to successfully run fMRIPrep on the HCP-Development and Young Adult data after turning the bids verification off. I have not tested the Aging dataset yet.
- suyashdb/hcp2bids
- Phase encoding direction discussion
- Russ Poldrack asking about HCP BIDS data on Twitter/X
- Neurostars question asking about JSON sidecar files for HCPYA. (PhaseEncodingDirection should be reversed from that provided by the asker.)
- Partial conversion script for converting the HCPYA data to BIDS
- Neurostars question asking for HCP BIDS data
- Slice timing for HCPYA
- Diffusion readout time