Skip to content

xnat2bids

Export DICOM images from an XNAT experiment to a BIDS compliant directory

Usage:

$ xnat2bids [OPTIONS] SESSION BIDS_ROOT_DIR

Arguments:

  • SESSION: XNAT Session ID, that is the Accession # for an experiment. [required]
  • BIDS_ROOT_DIR: Root output directory for exporting the files [required]

Options:

  • -u, --user TEXT: XNAT User
  • -p, --pass TEXT: XNAT Password

  • -h, --host TEXT: XNAT'sURL [default: https://xnat.bnc.brown.edu]

  • -S, --session-suffix TEXT: The session_suffix is initially set to -1. This will signify an unspecified session_suffix and default to sess-01. For multi-session studies, the session label will be pulled from XNAT [default: -1]

  • -f, --bidsmap-file TEXT: Bidsmap JSON file to correct sequence names [default: ]
  • -i, --includeseq INTEGER: Include this sequence only, this flag can specify multiple times [default: ]
  • -s, --skipseq INTEGER: Exclude this sequence, can be specified multiple times [default: ]
  • --log-id TEXT: ID or suffix to append to logfile. If empty, current date is used [default: current date - MM-DD-YYYY-HH-MM-SS]
  • -v, --verbose: Verbose level. This flag can be specified multiple times to increase verbosity [default: 0]
  • --overwrite: Remove directories where prior results for this session/participant [default: False]
  • --cleanup / --no-cleanup: Remove xnat-export folder and move logs to derivatives/xnat/logs [default: False]
  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.