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.

heudiconv 1.3.2                                   November 2024                                     HEUDICONV(1)