.. AUTO-GENERATED FILE -- DO NOT EDIT!

.. _example_reconst_dsid:


========================
DSI Deconvolution vs DSI
========================

An alternative method to DSI is the method proposed by [Canales10]_ which is
called DSI with Deconvolution. This algorithm is using Lucy-Richardson
deconvolution in the diffusion propagator with the goal to create sharper ODFs
with higher angular resolution.

In this example we will show with simulated data how this method's ODF performs
against standard DSI ODF and a ground truth multi tensor ODF.

::
  
  from dipy.sims.voxel import multi_tensor, multi_tensor_odf
  from dipy.data import get_data, get_sphere
  from dipy.core.gradients import gradient_table
  from dipy.reconst.dsi import (DiffusionSpectrumDeconvModel,
                                DiffusionSpectrumModel)
  

For the simulation we will use a standard DSI acqusition scheme with 514
gradient directions and 1 S0.

::
  
  btable = np.loadtxt(get_data('dsi515btable'))
  
  gtab = gradient_table(btable[:, 0], btable[:, 1:])
  

Let's create a multi tensor with 2 fiber directions at 60 degrees.

::
  
  evals = np.array([[0.0015, 0.0003, 0.0003],
                    [0.0015, 0.0003, 0.0003]])
  
  directions = [(-30, 0), (30, 0)]
  
  fractions = [50, 50]
  
  signal, _ = multi_tensor(gtab, evals, 100, angles=directions,
                           fractions=fractions, snr=None)
  
  sphere = get_sphere('symmetric724').subdivide(1)
  
  odf_gt = multi_tensor_odf(sphere.vertices, evals, angles=directions,
                            fractions=fractions)
  

Perform the reconstructions with standard DSI and DSI with deconvolution.

::
  
  dsi_model = DiffusionSpectrumModel(gtab)
  
  dsi_odf = dsi_model.fit(signal).odf(sphere)
  
  dsid_model = DiffusionSpectrumDeconvModel(gtab)
  
  dsid_odf = dsid_model.fit(signal).odf(sphere)
  

Finally, we can visualize the ground truth ODF, together with the DSI and DSI
with deconvolution ODFs and observe that with the deconvolved method it is
easier to resolve the correct fiber directions because the ODF is sharper.

::
  
  from dipy.viz import fvtk
  
  ren = fvtk.ren()
  
  odfs = np.vstack((odf_gt, dsi_odf, dsid_odf))[:, None, None]
  
  odf_actor = fvtk.sphere_funcs(odfs, sphere)
  odf_actor.RotateX(90)
  fvtk.add(ren, odf_actor)
  fvtk.record(ren, out_path='dsid.png', size=(300, 300))
  

.. figure:: dsid.png
    :align: center

    **Ground truth ODF (left), DSI ODF (middle), DSI with Deconvolution ODF(right)**

.. [Canales10] Canales-Rodriguez et al., Deconvolution in Diffusion Spectrum Imaging,
			   Neuroimage, vol 50, no 1, 136-149, 2010.


        
.. admonition:: Example source code

   You can download :download:`the full source code of this example <./reconst_dsid.py>`.
   This same script is also included in the dipy source distribution under the
   :file:`doc/examples/` directory.

