.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH HEUDICONV "1" "May 2023" "heudiconv 0.13.1" "User Commands"
.SH NAME
heudiconv \- DICOM converter for organizing brain imaging data into structured directory layouts
.SH DESCRIPTION
usage: heudiconv [\-h] [\-\-version]
.IP
[\-d DICOM_DIR_TEMPLATE | \fB\-\-files\fR [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]
.PP
Example: heudiconv \fB\-d\fR 'rawdata/{subject}' \fB\-o\fR . \fB\-f\fR heuristic.py \fB\-s\fR s1 s2 s3
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-d\fR DICOM_DIR_TEMPLATE, \fB\-\-dicom_dir_template\fR 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 \fB\-\-ses\fR argument is ignored. Note that
you might need to surround the value with quotes to
avoid {...} being considered by shell
.TP
\fB\-\-files\fR [FILES ...]
Files (tarballs, dicoms) or directories containing
files to process. Cannot be provided if using
\fB\-\-dicom_dir_template\fR.
.TP
\fB\-s\fR [SUBJS ...], \fB\-\-subjects\fR [SUBJS ...]
List of subjects \- required for dicom template. If not
provided, DICOMS would first be "sorted" and subject
IDs deduced by the heuristic.
.TP
\fB\-c\fR {dcm2niix,none}, \fB\-\-converter\fR {dcm2niix,none}
Tool to use for DICOM conversion. Setting to "none"
disables the actual conversion step \fB\-\-\fR useful for
testing heuristics.
.TP
\fB\-o\fR OUTDIR, \fB\-\-outdir\fR OUTDIR
Output directory for conversion setup (for further
customization and future reference. This directory
will refer to non\-anonymized subject IDs.
.TP
\fB\-l\fR LOCATOR, \fB\-\-locator\fR LOCATOR
Study path under outdir. If provided, it overloads the
value provided by the heuristic. If \fB\-\-datalad\fR is
enabled, every directory within locator becomes a
super\-dataset thus establishing a hierarchy. Setting
to "unknown" will skip that dataset.
.TP
\fB\-a\fR CONV_OUTDIR, \fB\-\-conv\-outdir\fR CONV_OUTDIR
Output directory for converted files. By default this
is identical to \fB\-\-outdir\fR. This option is most useful
in combination with \fB\-\-anon\-cmd\fR.
.TP
\fB\-\-anon\-cmd\fR 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
\fB\-\-conv\-outdir\fR.
.TP
\fB\-f\fR HEURISTIC, \fB\-\-heuristic\fR HEURISTIC
Name of a known heuristic or path to the Python script
containing heuristic.
.TP
\fB\-p\fR, \fB\-\-with\-prov\fR
Store additional provenance information. Requires
python\-rdflib.
.TP
\fB\-ss\fR SESSION, \fB\-\-ses\fR SESSION
Session for longitudinal study_sessions. Default is
None.
.TP
\fB\-b\fR [BIDSOPTION1 [BIDSOPTION2 ...]], \fB\-\-bids\fR [BIDSOPTION1 [BIDSOPTION2 ...]]
Flag for output into BIDS structure. Can also take
BIDS\-specific options, e.g., \fB\-\-bids\fR 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.
.TP
\fB\-\-overwrite\fR
Overwrite existing converted files.
.TP
\fB\-\-datalad\fR
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.
.TP
\fB\-\-dbg\fR
Do not catch exceptions and show exception traceback.
.TP
\fB\-\-command\fR {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.
.TP
\fB\-g\fR {studyUID,accession_number,all,custom}, \fB\-\-grouping\fR {studyUID,accession_number,all,custom}
How to group dicoms (default: by studyUID).
.TP
\fB\-\-minmeta\fR
Exclude dcmstack meta information in sidecar jsons.
.TP
\fB\-\-random\-seed\fR RANDOM_SEED
Random seed to initialize RNG.
.TP
\fB\-\-dcmconfig\fR DCMCONFIG
JSON file for additional dcm2niix configuration.
.SS "Conversion submission options:"
.TP
\fB\-q\fR {SLURM,None}, \fB\-\-queue\fR {SLURM,None}
Batch system to submit jobs in parallel.
.TP
\fB\-\-queue\-args\fR QUEUE_ARGS
Additional queue arguments passed as a single string
of space\-separated Argument=Value pairs.