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HCPLifespan2BIDS

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.

Lifespan

Usage

python lifepsan.py --nda_dir <path to unprocessed data> --output_dir <path to output BIDS directory>

Options

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.

Downloading the data

I found it easiest to use the ndatools downloadcmd commandline tool to download the data. You can download downloadcmd using pip install nda-tools.

HCP Young Adult

TODO: Add information about the HCP Young Adult dataset.

Running fMRIPrep

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.

Useful Links