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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
  • -i, --includeseq TEXT: Include this sequence only, this flag can specify multiple times
  • -s, --skipseq TEXT: Exclude this sequence, can be specified multiple times
  • --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
  • --cleanup: Remove xnat-export folder and move logs to derivatives/xnat/logs
  • --skip-export: Skip DICOM Export, while only running BIDS conversion
  • --export-only: Run DICOM Export without subsequent BIDS conversion
  • --validate_frames: Validate the frame counts of all acquisitions of functional bold sequences. If the final acquisition does not contain the expected number of slices, the associated DICOM file will be deleted.
  • -d, --dicomfix-config TEXT: JSON file to correct DICOM fields. USE WITH CAUTION
  • --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.