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 | list) bool ¶
Checks if all entries in a bvals file are zero (or 5, for Siemens files).
- Parameters:
bval_file (str) – file with the bvals
- 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: Callable[[str, tuple[str, ...], list[str]], Any] | None, with_prov: bool, bids_options: str | None, outdir: str, min_meta: bool, overwrite: bool, symlink: bool = True, prov_file: str | None = None, dcmconfig: str | None = None, populate_intended_for_opts: PopulateIntendedForOpts | None = None) None ¶
Perform actual conversion (calls to converter etc) given info from heuristic’s infotodict
- heudiconv.convert.convert_dicom(item_dicoms: list[str], bids_options: str | None, prefix: str, outdir: str, tempdirs: 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[str], prefix: str, with_prov: bool, bids_options: str | None, tmpdir: str, dcmconfig: str | None = None) tuple[Node, str | None] ¶
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: Node, item_dicoms: list[str], bids_options: str | None, outtype: str, prefix: str, outname_bids: str, overwrite: bool) list[str] ¶
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[str, Any], 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[str, Any], filename: str, echo_times: list[float]) 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[str, Any], filename: str, channel_names: list[str]) 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