kwneuro.masks
=============

.. py:module:: kwneuro.masks


Functions
---------

.. autoapisummary::

   kwneuro.masks.brain_extract_batch
   kwneuro.masks.brain_extract_single


Module Contents
---------------

.. py:function:: 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.

   :param 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`.


.. py:function:: 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`.

   :param dwi: Input DWI
   :param output_path: Output path for brain mask

   Returns the computed brain mask.