DICOMS

heudiconv.dicoms.compress_dicoms(dicom_list, out_prefix, tempdirs, overwrite)

Archives DICOMs into a tarball

Also tries to do it reproducibly, so takes the date for files and target tarball based on the series time (within the first file)

Parameters:
  • dicom_list (list of str) – list of dicom files
  • out_prefix (str) – output path prefix, including the portion of the output file name before .dicom.tgz suffix
  • tempdirs (object) – TempDirs object to handle multiple tmpdirs
  • overwrite (bool) – Overwrite existing tarfiles
Returns:

filename – Result tarball
Return type:

str
heudiconv.dicoms.create_seqinfo(mw, series_files, series_id)

Generate sequence info

Parameters:
  • mw (MosaicWrapper) –
  • series_files (list) –
  • series_id (str) –
heudiconv.dicoms.embed_dicom_and_nifti_metadata(dcmfiles, niftifile, infofile, bids_info)

Embed metadata from nifti (affine etc) and dicoms into infofile (json)

niftifile should exist. Its affine’s orientation information is used while establishing new NiftiImage out of dicom stack and together with bids_info (if provided) is dumped into json infofile

Parameters:
  • dcmfiles –
  • niftifile –
  • infofile –
  • bids_info (dict) – Additional metadata to be embedded. infofile is overwritten if exists, so here you could pass some metadata which would overload (at the first level of the dict structure, no recursive fancy updates) what is obtained from nifti and dicoms
heudiconv.dicoms.embed_metadata_from_dicoms(bids_options, item_dicoms, outname, outname_bids, prov_file, scaninfo, tempdirs, with_prov)

Enhance sidecar information file with more information from DICOMs

Parameters:
  • bids_options –
  • item_dicoms –
  • outname –
  • outname_bids –
  • prov_file –
  • scaninfo –
  • tempdirs –
  • with_prov –
heudiconv.dicoms.get_dicom_series_time(dicom_list)

Get time in seconds since epoch from dicom series date and time Primarily to be used for reproducible time stamping

heudiconv.dicoms.group_dicoms_into_seqinfos(files, grouping, file_filter=None, dcmfilter=None, flatten=False, custom_grouping=None)

Process list of dicoms and return seqinfo and file group seqinfo contains per-sequence extract of fields from DICOMs which will be later provided into heuristics to decide on filenames

Parameters:
  • files (list of str) – List of files to consider
  • grouping ({'studyUID', 'accession_number', 'all', 'custom'}) – How to group DICOMs for conversion. If ‘custom’, see custom_grouping parameter.
  • file_filter (callable, optional) – Applied to each item of filenames. Should return True if file needs to be kept, False otherwise.
  • dcmfilter (callable, optional) – If called on dcm_data and returns True, it is used to set series_id
  • flatten (bool, optional) – Creates a flattened seqinfo with corresponding DICOM files. True when invoked with dicom_dir_template.
  • custom_grouping (str or callable, optional) – grouping key defined within heuristic. Can be a string of a DICOM attribute, or a method that handles more complex groupings.
Returns:

  • seqinfo (list of list) – seqinfo is a list of info entries per each sequence (some entry there defines a key for filegrp)
  • filegrp (dict) – filegrp is a dictionary with files grouped per each sequence
heudiconv.dicoms.parse_private_csa_header(dcm_data, public_attr, private_attr, default=None)

Parses CSA header in cases where value is not defined publicly

Parameters:
  • dcm_data (pydicom Dataset object) – DICOM metadata
  • public_attr (string) – non-private DICOM attribute
  • private_attr (string) – private DICOM attribute
  • (optional) (default) – default value if private_attr not found
Returns:

val (default – private attribute value or default
Return type:

empty string)
heudiconv.dicoms.validate_dicom(fl, dcmfilter)

Parse DICOM attributes. Returns None if not valid.