Conversion

heudiconv.convert.add_taskname_to_infofile(infofiles)

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)

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, converter, scaninfo_suffix, custom_callable, with_prov, bids_options, outdir, min_meta, overwrite, symlink=True, prov_file=None, dcmconfig=None, populate_intended_for_opts={})

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

heudiconv.convert.convert_dicom(item_dicoms, bids_options, prefix, outdir, tempdirs, symlink, overwrite)

Save DICOMs as output (default is by symbolic link)

Parameters:
  • item_dicoms (list of filenames) – DICOMs to save
  • bids_options (list or None) – If not None then save to BIDS format. List 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, prefix, with_prov, bids_options, tmpdir, dcmconfig=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 (list or None) – If not None then output BIDS sidecar JSONs List 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, item_dicoms, bids_options, outtype, prefix, outname_bids, overwrite)

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, filename)

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, filename, echo_times)

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, filename, channel_names)

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