kwneuro.tractseg
================

.. py:module:: kwneuro.tractseg


Functions
---------

.. autoapisummary::

   kwneuro.tractseg.extract_tractseg


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

.. py:function:: extract_tractseg(dwi: kwneuro.dwi.Dwi, mask: kwneuro.resource.VolumeResource, response: kwneuro.resource.ResponseFunctionResource | None = None, output_type: str = 'tract_segmentation') -> kwneuro.resource.VolumeResource

   Run TractSeg on a DWI dataset to segment white matter tracts.

   :param dwi: The Diffusion Weighted Imaging (DWI) dataset.
   :param mask: A binary brain mask volume.
   :param response: The single-fiber response function. If `None`, the response function is estimated using an ROI in the center of the brain mask.
   :type response: Optional
   :param output_type: TractSeg can segment not only bundles, but also the end regions of bundles.
                       Moreover it can create Tract Orientation Maps (TOM).
                       'tract_segmentation' [DEFAULT]: Segmentation of bundles (72 bundles).
                       'endings_segmentation': Segmentation of bundle end regions (72 bundles).
                       'TOM': Tract Orientation Maps (20 bundles).

   Returns: A volume resource containing a 4D numpy array with the output of tractseg
       for tract_segmentation:     [x, y, z, nr_of_bundles]
       for endings_segmentation:   [x, y, z, 2*nr_of_bundles]
       for TOM:                    [x, y, z, 3*nr_of_bundles]