kwneuro.dwi
===========

.. py:module:: kwneuro.dwi


Classes
-------

.. autoapisummary::

   kwneuro.dwi.Dwi


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

.. py:class:: Dwi

   A diffusion weighted image.


   .. py:attribute:: volume
      :type:  kwneuro.resource.VolumeResource

      The DWI image volume.
      It is assumed to be a 4D volume, with the first three dimensions being spatial and the final dimension indexing
      the diffusion weightings.


   .. py:attribute:: bval
      :type:  kwneuro.resource.BvalResource

      The DWI b-values


   .. py:attribute:: bvec
      :type:  kwneuro.resource.BvecResource

      The DWI b-vectors


   .. py:method:: load() -> Dwi

      Load any on-disk resources into memory and return a Dwi with all loadable resources loaded.



   .. py:method:: save(path: kwneuro.util.PathLike, basename: str) -> Dwi

      Save all resources to disk and return a Dwi with all resources being on-disk.

      :param path: The desired save directory.
      :param basename: The desired file basenames, i.e. without an extension.

      Returns: A Dwi with its internal resources being on-disk.



   .. py:method:: get_gtab() -> dipy.core.gradients.GradientTable

      Get the GradientTable for this DWI.



   .. py:method:: compute_mean_b0() -> kwneuro.resource.InMemoryVolumeResource

      Compute the mean of the b=0 images of a DWI.



   .. py:method:: concatenate(dwis: list[Dwi]) -> Dwi
      :staticmethod:


      Concatenate a list of ``Dwi``\s into a single (loaded) DWI.

      The affine and metadata of the first ``Dwi`` in the list will be used to concatenate volumes.



   .. py:method:: denoise() -> Dwi

      Denoise using Patch2Self from DIPY.



   .. py:method:: extract_brain() -> kwneuro.resource.InMemoryVolumeResource

      Extract brain mask. This is meant to be convenient rather than efficient.
      Using this in a loop could result in unnecessary repetition of file I/O operations.
      For efficiency, see :func:`kwneuro.masks.brain_extract_batch`.



   .. py:method:: estimate_dti(mask: kwneuro.resource.VolumeResource | None = None) -> kwneuro.dti.Dti

      Estimate diffusion tensor image from this DWI



   .. py:method:: estimate_noddi(mask: kwneuro.resource.VolumeResource | None = None, dpar: float = 0.0017, n_kernel_dirs: int = 500) -> kwneuro.noddi.Noddi

      Estimate NODDI model parameters from this DWI. See :meth:`kwneuro.noddi.Noddi.estimate_from_dwi` for details.