Conversion¶
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heudiconv.convert.add_taskname_to_infofile(infofiles)¶ Add the “TaskName” field to json files corresponding to func images.
infofiles : list with json filenames or single filename
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heudiconv.convert.bvals_are_zero(bval_file)¶ Checks if all entries in a bvals file are zero (or 5, for Siemens files). Returns True if that is the case, otherwise returns False
bval_file : file with the bvals
True if all are zero; False otherwise.
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heudiconv.convert.convert(items, converter, scaninfo_suffix, custom_callable, with_prov, bids_options, outdir, min_meta, overwrite, symlink=True, prov_file=None, dcmconfig=None)¶ Perform actual conversion (calls to converter etc) given info from heuristic’s infotodict
items symlink converter scaninfo_suffix custom_callable with_prov is_bids sourcedir outdir min_meta
None
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heudiconv.convert.convert_dicom(item_dicoms, bids_options, prefix, outdir, tempdirs, symlink, overwrite)¶ Save DICOMs as output (default is by symbolic link)
- 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
None
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heudiconv.convert.nipype_convert(item_dicoms, prefix, with_prov, bids_options, tmpdir, dcmconfig=None)¶ Converts DICOMs grouped from heuristic using Nipype’s Dcm2niix interface.
- item_dicoms : List
- DICOM files to convert
- prefix : String
- 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 : Directory
- Conversion working directory
- dcmconfig : File (optional)
- JSON file used for additional Dcm2niix configuration
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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.
- res : Node
- Nipype conversion Node with results
- item_dicoms: list of filenames
- DICOMs converted
- bids : list or None
- If not list save to BIDS List may contain bids specific options
prefix : string
- bids_outfiles
- Converted BIDS files
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heudiconv.convert.update_complex_name(metadata, filename, suffix)¶ Insert _part-<mag|phase> entity into filename if data are from a sequence with magnitude/phase part.
- metadata : dict
- Scan metadata dictionary from BIDS sidecar file.
- filename : str
- Incoming filename
- suffix : str
- An index used for cases where a single scan produces multiple files, but the differences between those files are unknown.
- filename : str
- Updated filename with rec entity added in appropriate position.
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heudiconv.convert.update_multiecho_name(metadata, filename, echo_times)¶ Insert _echo-<num> entity into filename if data are from a multi-echo sequence.
- 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.
- filename : str
- Updated filename with echo entity added, if appropriate.
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heudiconv.convert.update_uncombined_name(metadata, filename, channel_names)¶ Insert _ch-<num> entity into filename if data are from a sequence with “save uncombined”.
- 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.
- filename : str
- Updated filename with ch entity added, if appropriate.