Conversion

heudiconv.convert.add_taskname_to_infofile(infofiles: str | list[str]) → None

Add the “TaskName” field to json files with _task- entity in the name.

Note: _task- entity could be present not only in functional data but in many other modalities now.

Parameters:infofiles (list or str) – json filenames or a single filename.
heudiconv.convert.bvals_are_zero(bval_file: str) → bool

Checks if all entries in a bvals file are zero (or 5, for Siemens files).

Parameters:bval_file (str) – file with the bvals
Returns:
Return type:True if all are all 0 or 5; False otherwise.
heudiconv.convert.convert(items: list[tuple[str, tuple[str, ...], list[str]]], converter: str, scaninfo_suffix: str, custom_callable: Optional[Callable[[str, tuple[str, ...], list[str]], Any]], with_prov: bool, bids_options: Optional[str], outdir: str, min_meta: bool, overwrite: bool, symlink: bool = True, prov_file: Optional[str] = None, dcmconfig: Optional[str] = None, populate_intended_for_opts: Optional[PopulateIntendedForOpts] = None) → None

Perform actual conversion (calls to converter etc) given info from heuristic’s infotodict

heudiconv.convert.convert_dicom(item_dicoms: list, bids_options: Optional[str], prefix: str, outdir: str, tempdirs: heudiconv.utils.TempDirs, _symlink: bool, overwrite: bool) → None

Save DICOMs as output (default is by symbolic link)

Parameters:
  • item_dicoms (list of filenames) – DICOMs to save
  • bids_options (str or None) – If not None then save to BIDS format. String may be empty or contain bids specific options
  • prefix (string) – Conversion outname
  • outdir (string) – Output directory
  • tempdirs (TempDirs instance) – Object to handle temporary directories created TODO: remove
  • symlink (bool) – Create softlink to DICOMs - if False, create hardlink instead.
  • overwrite (bool) – If True, allows overwriting of previous conversion
heudiconv.convert.nipype_convert(item_dicoms: list, prefix: str, with_prov: bool, bids_options: Optional[str], tmpdir: str, dcmconfig: Optional[str] = None) → tuple

Converts DICOMs grouped from heuristic using Nipype’s Dcm2niix interface.

Parameters:
  • item_dicoms (list) – DICOM files to convert
  • prefix (str) – Heuristic output path
  • with_prov (bool) – Store provenance information
  • bids_options (str or None) – If not None then output BIDS sidecar JSONs String may contain bids specific options
  • tmpdir (str) – Conversion working directory
  • dcmconfig (str, optional) – JSON file used for additional Dcm2niix configuration
heudiconv.convert.save_converted_files(res: nipype.pipeline.engine.nodes.Node, item_dicoms: list, bids_options: Optional[str], outtype: str, prefix: str, outname_bids: str, overwrite: bool) → list

Copy converted files from tempdir to output directory.

Will rename files if necessary.

Parameters:
  • res (Node) – Nipype conversion Node with results
  • item_dicoms (list) – Filenames of converted DICOMs
  • bids (list or None) – If not list save to BIDS List may contain bids specific options
  • prefix (str) –
Returns:

Converted BIDS files
Return type:

bids_outfiles
heudiconv.convert.update_complex_name(metadata: dict, filename: str) → str

Insert _part-<mag|phase> entity into filename if data are from a sequence with magnitude/phase part.

Parameters:
  • metadata (dict) – Scan metadata dictionary from BIDS sidecar file.
  • filename (str) – Incoming filename
Returns:

filename – Updated filename with part entity added in appropriate position.
Return type:

str
heudiconv.convert.update_multiecho_name(metadata: dict, filename: str, echo_times: list) → str

Insert _echo-<num> entity into filename if data are from a multi-echo sequence.

Parameters:
  • metadata (dict) – Scan metadata dictionary from BIDS sidecar file.
  • filename (str) – Incoming filename
  • echo_times (list) – List of all echo times from scan. Used to determine the echo number (i.e., index) if field is missing from metadata.
Returns:

filename – Updated filename with echo entity added, if appropriate.
Return type:

str
heudiconv.convert.update_uncombined_name(metadata: dict, filename: str, channel_names: list) → str

Insert _ch-<num> entity into filename if data are from a sequence with “save uncombined”.

Parameters:
  • metadata (dict) – Scan metadata dictionary from BIDS sidecar file.
  • filename (str) – Incoming filename
  • channel_names (list) – List of all channel names from scan. Used to determine the channel number (i.e., index) if field is missing from metadata.
Returns:

filename – Updated filename with ch entity added, if appropriate.
Return type:

str