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}]   [-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

   optional arguments:
       -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}
              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.