kwneuro.run
===========

.. py:module:: kwneuro.run

.. autoapi-nested-parse::

   .. click:: kwneuro.run:gen_masks
       :prog: gen_masks
       :nested: short



Functions
---------

.. autoapisummary::

   kwneuro.run.gen_masks


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

.. py:function:: gen_masks(inputs: pathlib.Path, outputs: pathlib.Path) -> None

   Recursively find and process dwi images and create hd_bet masks for each.
   Preserves directory structure in output.

   Searches for input files: ``<ID>_dwi.nii.gz``, ``<ID>.bval``, ``<ID>.bvec``

   Produces output files: ``<ID>_mask.nii.gz``


   See :func:`kwneuro.masks.brain_extract_batch` for details.