kwneuro.noddi
=============

.. py:module:: kwneuro.noddi


Classes
-------

.. autoapisummary::

   kwneuro.noddi.Noddi


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

.. py:class:: Noddi

   A Noddi result


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

      The NODDI image volume.
      It is a 4D volume, with the first three dimensions being spatial and the final dimension indexing
      the noddi outputs.


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

      The NODDI image volume.
      It is a 4D volume, with the first three dimensions being spatial and the final dimension indexing
      the directions.


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

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



   .. py:method:: save(path: kwneuro.util.PathLike) -> Noddi

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

      :param path: The desired file save location, a nifti file path.

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



   .. py:method:: estimate_from_dwi(dwi: kwneuro.dwi.Dwi, mask: kwneuro.resource.VolumeResource | None = None, dpar: float = 0.0017, n_kernel_dirs: int = 500) -> Noddi
      :staticmethod:


      Estimate Noddi from a DWI.

      :param dwi: The source DWI
      :param mask: Optionally, a boolean 3D volume that has indicates where the fit should take place,
                   such as a brain mask.
      :param dpar: The parallel diffusivity to be used in the model fitting. If not provided, the default value of
                   1.7e-3 mm^2/s is used, which is suitable for white matter. For gray matter, a value of 1.3e-3 mm^2/s is recommended.
      :param n_kernel_dirs: The number of directions to use when generating the AMICO NODDI kernels. This value represents the total
                            count of possible orientations for the response functions across the half-sphere. Default: 500.

      Returns: A Noddi resource containing the estimated parameters.



   .. py:property:: ndi
      :type: kwneuro.resource.VolumeResource


      Neurite Density Index (NDI) map as a 3D volume.


   .. py:property:: odi
      :type: kwneuro.resource.VolumeResource


      Orientation Dispersion Index (ODI) map as a 3D volume.


   .. py:property:: fwf
      :type: kwneuro.resource.VolumeResource


      Free Water Fraction (FWF) map as a 3D volume.


   .. py:method:: get_modulated_ndi_odi() -> tuple[kwneuro.resource.VolumeResource, kwneuro.resource.VolumeResource]

      Compute the modulated maps, NDI*TF and ODI*TF, where TF = 1 - FWF.

      :returns: Returns 3D volumes for modulated NDI and ODI maps, as VolumeResources.