kwneuro.masks

Functions

brain_extract_batch(→ list[kwneuro.io.NiftiVolumeResource])	Run brain extraction on a batch of cases.
brain_extract_single(→ kwneuro.io.NiftiVolumeResource)	Run brain extraction on a single case.

Module Contents

kwneuro.masks.brain_extract_batch(cases: list[tuple[kwneuro.dwi.Dwi, pathlib.Path]]) → list[kwneuro.io.NiftiVolumeResource]

Run brain extraction on a batch of cases. HD-BET does not run in parallel, but it does have some initialization time so it helps to run cases in batches.

Parameters:

cases – A list of pairs each consisting of an input Dwi and desired output path for the mask.

Returns a list of computed brain masks that is in correspondence with the list of input cases.

kwneuro.masks.brain_extract_single(dwi: kwneuro.dwi.Dwi, output_path: kwneuro.util.PathLike) → kwneuro.io.NiftiVolumeResource

Run brain extraction on a single case.

HD-BET has significant initialization time, so it is not advised to run this function in a loop; see brain_extract_batch.

Parameters:

• dwi – Input DWI

• output_path – Output path for brain mask

Returns the computed brain mask.