HEUDICONV

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:

-h, --help

show this help message and exit

--version

show program’s version number and exit

-d DICOM_DIR_TEMPLATE, --dicom_dir_template DICOM_DIR_TEMPLATE

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 [FILES ...]

Files (tarballs, dicoms) or directories containing files to process. Cannot be provided if using --dicom_dir_template.

-s [SUBJS ...], --subjects [SUBJS ...]

List of subjects - required for dicom template. If not provided, DICOMS would first be "sorted" and subject IDs deduced by the heuristic.

-c {dcm2niix,none}, --converter {dcm2niix,none}

Tool to use for DICOM conversion. Setting to "none" disables the actual conversion step -- useful for testing heuristics.

-o OUTDIR, --outdir OUTDIR

Output directory for conversion setup (for further customization and future reference. This directory will refer to non-anonymized subject IDs.

-l LOCATOR, --locator LOCATOR

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.

-a CONV_OUTDIR, --conv-outdir CONV_OUTDIR

Output directory for converted files. By default this is identical to --outdir. This option is most useful in combination with --anon-cmd.

--anon-cmd 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.

-f HEURISTIC, --heuristic HEURISTIC

Name of a known heuristic or path to the Python script containing heuristic.

-p, --with-prov

Store additional provenance information. Requires python-rdflib.

-ss SESSION, --ses SESSION

Session for longitudinal study_sessions. Default is None.

-b [BIDSOPTION1 [BIDSOPTION2 ...]], --bids [BIDSOPTION1 [BIDSOPTION2 ...]]

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

Overwrite existing converted files.

--datalad

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.

--dbg

Do not catch exceptions and show exception traceback.

--command
{heuristics,heuristic-info,ls,populate-templates,sanitize-jsons,treat-jsons,populate-intended-for}

Custom action to be performed on provided files instead of regular operation.

-g {studyUID,accession_number,all,custom}, --grouping
{studyUID,accession_number,all,custom}

How to group dicoms (default: by studyUID).

--minmeta

Exclude dcmstack meta information in sidecar jsons.

--random-seed RANDOM_SEED

Random seed to initialize RNG.

--dcmconfig DCMCONFIG

JSON file for additional dcm2niix configuration.

Conversion submission options:

-q {SLURM,None}, --queue {SLURM,None}

Batch system to submit jobs in parallel.

--queue-args QUEUE_ARGS

Additional queue arguments passed as a single string of space-separated Argument=Value pairs.