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HEUDICONV(1) User Commands HEUDICONV(1)

NAME

heudiconv - DICOM converter for organizing brain imaging data into structured directory layouts

DESCRIPTION

usage: heudiconv [-h] [--version]

[-d DICOM_DIR_TEMPLATE | --files [FILES ...]] [-s [SUBJS ...]] [-c {dcm2niix,none}] [-o OUTDIR] [-l LOCATOR] [-a CONV_OUTDIR] [--anon-cmd ANON_CMD] [-f HEURISTIC] [-p] [-ss SESSION] [-b [BIDSOPTION1 [BIDSOPTION2 ...]]] [--overwrite] [--datalad] [--dbg] [--command {heuristics,heuristic-info,ls,populate-templates,sanitize-jsons,treat-jsons,populate-intended-for}] [-g {studyUID,accession_number,all,custom}] [--minmeta] [--random-seed RANDOM_SEED] [--dcmconfig DCMCONFIG] [-q {SLURM,None}] [--queue-args QUEUE_ARGS]

Example: heudiconv -d 'rawdata/{subject}' -o . -f heuristic.py -s s1 s2 s3

options:

show this help message and exit
show program's version number and exit
Location of dicomdir that can be indexed with subject id {subject} and session {session}. Tarballs (can be compressed) are supported in addition to directory. All matching tarballs for a subject are extracted and their content processed in a single pass. If multiple tarballs are found, each is assumed to be a separate session and the --ses argument is ignored. Note that you might need to surround the value with quotes to avoid {...} being considered by shell
Files (tarballs, dicoms) or directories containing files to process. Cannot be provided if using --dicom_dir_template.
List of subjects - required for dicom template. If not provided, DICOMS would first be "sorted" and subject IDs deduced by the heuristic.
Tool to use for DICOM conversion. Setting to "none" disables the actual conversion step -- useful for testing heuristics.
Output directory for conversion setup (for further customization and future reference. This directory will refer to non-anonymized subject IDs.
Study path under outdir. If provided, it overloads the value provided by the heuristic. If --datalad is enabled, every directory within locator becomes a super-dataset thus establishing a hierarchy. Setting to "unknown" will skip that dataset.
Output directory for converted files. By default this is identical to --outdir. This option is most useful in combination with --anon-cmd.
Command to run to convert subject IDs used for DICOMs to anonymized IDs. Such command must take a single argument and return a single anonymized ID. Also see --conv-outdir.
Name of a known heuristic or path to the Python script containing heuristic.
Store additional provenance information. Requires python-rdflib.
Session for longitudinal study_sessions. Default is None.
Flag for output into BIDS structure. Can also take BIDS-specific options, e.g., --bids notop. The only currently supported options is "notop", which skips creation of top-level BIDS files. This is useful when running in batch mode to prevent possible race conditions.
Overwrite existing converted files.
Store the entire collection as DataLad dataset(s). Small files will be committed directly to git, while large to annex. New version (6) of annex repositories will be used in a "thin" mode so it would look to mortals as just any other regular directory (i.e. no symlinks to under .git/annex). For now just for BIDS mode.
Do not catch exceptions and show exception traceback.
Custom action to be performed on provided files instead of regular operation.
How to group dicoms (default: by studyUID).
Exclude dcmstack meta information in sidecar jsons.
Random seed to initialize RNG.
JSON file for additional dcm2niix configuration.

Conversion submission options:

Batch system to submit jobs in parallel.
Additional queue arguments passed as a single string of space-separated Argument=Value pairs.
May 2024 heudiconv 1.1.1