Provided by: heudiconv_0.5.3-1_all bug

NAME

       dicoms.py:7: - DICOM converter for organizing brain imaging data into structured directory
       layouts

DESCRIPTION

       /build/heudiconv-SAT495/heudiconv-0.5.3/debian/heudiconv/usr/lib/python2.7/dist-packages/heudiconv/dicoms.py:7:
       UserWarning:  The  DICOM  readers  are  highly  experimental,  unstable, and only work for
       Siemens time-series at the moment Please use with caution.  We would be grateful for  your
       help in improving them

              from nibabel.nicom import csareader

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

              [-d DICOM_DIR_TEMPLATE | --files [FILES [FILES ...]]]  [-s [SUBJS [SUBJS ...]]] [-c
              {dcm2niix,none}] [-o OUTDIR] [-l LOCATOR] [-a  CONV_OUTDIR]  [--anon-cmd  ANON_CMD]
              [-f HEURISTIC] [-p] [-ss SESSION] [-b] [--overwrite] [--datalad] [--dbg] [--command
              {heuristics,heuristic-info,ls,populate-templates,sanitize-jsons,treat-jsons}]   [-g
              {studyUID,accession_number}]  [--minmeta]  [--random-seed  RANDOM_SEED]  [-q QUEUE]
              [--sbargs SBATCH_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

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

       -s [SUBJS [SUBJS ...]], --subjects [SUBJS [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 -- usefulfor 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 Pythonscript 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, --bids
              flag for output into BIDS structure

       --overwrite
              flag to allow overwriting 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 actions to be performed on provided files instead of regular operation.

       -g {studyUID,accession_number}, --grouping {studyUID,accession_number}
              How to group dicoms (default: by studyUID)

       --minmeta
              Exclude dcmstack meta information in sidecar jsons

       --random-seed RANDOM_SEED
              Random seed to initialize RNG

   Conversion submission options:
       -q QUEUE, --queue QUEUE
              select batch system to submit jobs to instead of running the conversion serially

       --sbargs SBATCH_ARGS
              Additional sbatch arguments if running with queue arg

       Please use with caution.  We would be grateful for your help in improving them

              from nibabel.nicom import csareader

       0.5.3

dicoms.py:7: UserWarning: The DICOM readersJanuaryg2019experimental, unstable, andDICOMS.PY:7:(1)Siemens time-series at the moment