Processing steps
================

MouseFlow pipeline consist of 9 different steps for the diffusion
weighted image (DWI) processing.

.. image:: ../data/mouseflow_graph.png
   :scale: 40 %
   :align: right

Input
-----
    * Diffusion weighted image (DWI)
    * b-values
    * b-vectors

DWI processes
-------------
    * Brain extraction (FSL)
    * Denoising (Mrtrix3)
    * Eddy (FSL)
    * N4 bias correction (ANTs)
    * Resample (Dipy)
    * DTI metrics (Dipy)
    * QBALL metrics (Dipy)

Tractography
------------
    * Local tracking