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

.. _example_brain_extraction_dwi:


===================================
Brain segmentation with median_otsu
===================================

We show how to extract brain information and mask from a b0 image using DIPY_'s
``segment.mask`` module.

First import the necessary modules:

::
  
  import numpy as np
  import nibabel as nib
  

Download and read the data for this tutorial.

The ``scil_b0`` dataset contains different data from different companies and
models. For this example, the data comes from a 1.5 Tesla Siemens MRI.

::
  
  from dipy.data.fetcher import fetch_scil_b0, read_siemens_scil_b0
  fetch_scil_b0()
  img = read_siemens_scil_b0()
  data = np.squeeze(img.get_data())
  

``img`` contains a nibabel Nifti1Image object. Data is the actual brain data as
a numpy ndarray.

Segment the brain using DIPY's ``mask`` module.

``median_otsu`` returns the segmented brain data and a binary mask of the brain.
It is possible to fine tune the parameters of ``median_otsu`` (``median_radius``
and ``num_pass``) if extraction yields incorrect results but the default
parameters work well on most volumes. For this example, we used 2 as
``median_radius`` and 1 as ``num_pass``

::
  
  from dipy.segment.mask import median_otsu
  b0_mask, mask = median_otsu(data, median_radius=2, numpass=1)
  

Saving the segmentation results is very easy using nibabel. We need the
``b0_mask``, and the binary mask volumes. The affine matrix which transform the
image's coordinates to the world coordinates is also needed. Here, we choose to
save both images in ``float32``.

::
  
  mask_img = nib.Nifti1Image(mask.astype(np.float32), img.affine)
  b0_img = nib.Nifti1Image(b0_mask.astype(np.float32), img.affine)
  
  fname = 'se_1.5t'
  nib.save(mask_img, fname + '_binary_mask.nii.gz')
  nib.save(b0_img, fname + '_mask.nii.gz')
  

Quick view of the results middle slice using ``matplotlib``.

::
  
  import matplotlib.pyplot as plt
  from dipy.core.histeq import histeq
  
  sli = data.shape[2] // 2
  plt.figure('Brain segmentation')
  plt.subplot(1, 2, 1).set_axis_off()
  plt.imshow(histeq(data[:, :, sli].astype('float')).T,
             cmap='gray', origin='lower')
  
  plt.subplot(1, 2, 2).set_axis_off()
  plt.imshow(histeq(b0_mask[:, :, sli].astype('float')).T,
             cmap='gray', origin='lower')
  
  plt.savefig('median_otsu.png')
  

.. figure:: median_otsu.png
   :align: center

   An application of median_otsu for brain segmentation.

``median_otsu`` can also automatically crop the outputs to remove the largest
possible number of background voxels. This makes outputted data significantly
smaller. Auto-cropping in ``median_otsu`` is activated by setting the
``autocrop`` parameter to ``True``.

::
  
  b0_mask_crop, mask_crop = median_otsu(data, median_radius=4, numpass=4,
                                        autocrop=True)
  

Saving cropped data using nibabel as demonstrated previously.

.. include:: ../links_names.inc

::
  
  mask_img_crop = nib.Nifti1Image(mask_crop.astype(np.float32), img.affine)
  b0_img_crop = nib.Nifti1Image(
      b0_mask_crop.astype(np.float32), img.affine)
  nib.save(mask_img_crop, fname + '_binary_mask_crop.nii.gz')
  nib.save(b0_img_crop, fname + '_mask_crop.nii.gz')
  


.. admonition:: Example source code

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