Heuristic

The heuristic file controls how information about the DICOMs is used to convert to a file system layout (e.g., BIDS). heudiconv includes some built-in heuristics, including ReproIn (which is great to adopt if you will be starting your data collection!).

However, there is a large variety of data out there, and not all DICOMs will be covered by the existing heuristics. This section will outline what makes up a heuristic file, and some useful functions available when making one.

Components

infotodict(seqinfos)

The only required function for a heuristic, infotodict is used to both define the conversion outputs and specify the criteria for scan to output association. Conversion outputs are defined as keys, a tuple consisting of a template path used for the basis of outputs, as well as a tuple of output types. Valid types include nii, nii.gz, and dicom.

Note

An example conversion key

('sub-{subject}/func/sub-{subject}_task-test_run-{item}_bold', ('nii.gz', 'dicom'))

The seqinfos parameter is a list of namedtuples which serves as a grouped and stacked record of the DICOMs passed in. Each item in seqinfo contains DICOM metadata that can be used to isolate the series, and assign it to a conversion key.

A dictionary of {conversion key: seqinfo} is returned.

create_key(template, outtype)

A common helper function used to create the conversion key in infotodict.

filter_files(fl)

A utility function used to filter any input files.

If this function is included, every file found will go through this filter. Any files where this function returns True will be filtered out.

filter_dicom(dcm_data)

A utility function used to filter any DICOMs.

If this function is included, every DICOM found will go through this filter. Any DICOMs where this function returns True will be filtered out.

infotoids(seqinfos, outdir)

Further processing on seqinfos to deduce/customize subject, session, and locator.

A dictionary of {“locator”: locator, “session”: session, “subject”: subject} is returned.