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dicom_export

Export XNAT DICOM images in an experiment to a BIDS friendly format

Usage:

$ dicom_export [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 <str>: XNAT User
  • -p, --pass <str>: XNAT Password
  • -h, --host <str>: XNAT's URL [default: https://xnat.bnc.brown.edu]
  • -S, --session-suffix <str>: 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 <str>: Bidsmap JSON file to correct sequence names
  • -i, --includeseq <str>: Include this sequence only, this flag can specify multiple times
  • -s, --skipseq <str>: Exclude this sequence, this flag can specify multiple times
  • --log-id <str>: 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. Can be specified multiple times to increase verbosity [default: 0]
  • --overwrite: Remove directories where prior results for session/participant may exist
  • --validate_frames: Validate frame counts for all BOLD sequence acquisitions. Deletes the DICOM file if the final acquisition lacks expected slices.
  • -d, --dicomfix-config <str>: JSON file to correct DICOM fields. USE WITH CAUTION
  • --force-non-defaced: Export original DICOM when REFACED_DICOM is available
  • --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.