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

.. _example_piesno:


=============================
Noise estimation using PIESNO
=============================

Often, one is interested in estimating the noise in the diffusion signal. One
of the methods to do this is the Probabilistic Identification and Estimation of
Noise (PIESNO) framework [Koay2009]_. Using this method, one can detect the
standard deviation of the noise from diffusion-weighted imaging (DWI). PIESNO
also works with multiple channel DWI datasets that are acquired from N array
coils for both SENSE and GRAPPA reconstructions.

The PIESNO method works in two steps:

1) First, it finds voxels that are most likely background voxels. Intuitively,
these voxels have very similar diffusion-weighted intensities (up to some noise)
in the fourth dimension of the DWI dataset. White matter, gray matter or CSF
voxels have diffusion intensities that vary quite a lot across different
directions.

2) From these estimated background voxels and the input number of coils N,
PIESNO finds what sigma each Gaussian from each of the N coils would have
generated the observed Rician (N=1) or non-central Chi (N>1) distributed noise
profile in the DWI datasets.

PIESNO makes an important assumption: the Gaussian noise standard deviation is
assumed to be uniform. The noise is uniform across multiple slice locations or
across multiple images of the same location.

For the full details, please refer to the original paper.

In this example, we will demonstrate the use of PIESNO with a 3-shell data-set.

We start by importing necessary modules and functions and loading the data:

::
  
  import nibabel as nib
  import numpy as np
  from dipy.denoise.noise_estimate import piesno
  from dipy.data import fetch_sherbrooke_3shell, read_sherbrooke_3shell
  
  
  fetch_sherbrooke_3shell()
  img, gtab = read_sherbrooke_3shell()
  data = img.get_data()
  

Now that we have fetched a dataset, we must call PIESNO with the right number
of coils used to acquire this dataset. It is also important to know what
was the parallel reconstruction algorithm used. Here, the data comes from a
GRAPPA reconstruction, was acquired with a 12-elements head coil available on
the Tim Trio Siemens, for which the 12 coil elements are combined into 4 groups
of 3 coil elements each. The signal is therefore received through 4 distinct
groups of receiver channels, yielding N = 4. Had we used a GE acquisition, we
would have used N=1 even if multiple channel coils are used because GE uses a
SENSE reconstruction, which has a Rician noise nature and thus N is always 1.

::
  
  sigma, mask = piesno(data, N=4, return_mask=True)
  
  axial = data[:, :, data.shape[2] / 2, 0].T
  axial_piesno = mask[:, :, data.shape[2] / 2].T
  
  import matplotlib.pyplot as plt
  fig, ax = plt.subplots(1, 2)
  ax[0].imshow(axial, cmap='gray', origin='lower')
  ax[0].set_title('Axial slice of the b=0 data')
  ax[1].imshow(axial_piesno, cmap='gray', origin='lower')
  ax[1].set_title('Background voxels from the data')
  for a in ax:
      a.set_axis_off()
  
  plt.savefig('piesno.png', bbox_inches='tight')
  

.. figure:: piesno.png
   :align: center

   **Showing the mid axial slice of the b=0 image (left) and estimated
   background voxels (right) used to estimate the noise standard deviation**.

::
  
  nib.save(nib.Nifti1Image(mask, img.get_affine(), img.get_header()),
           'mask_piesno.nii.gz')
  
  print('The noise standard deviation is sigma= ', sigma)
  print('The std of the background is =', np.std(data[mask[...,None].astype(np.bool)]))
  


Here, we obtained a noise standard deviation of 7.26. For comparison, a simple
standard deviation of all voxels in the estimated mask (as done in the previous
example :ref:`example_snr_in_cc`) gives a value of 6.1.


::
  


.. [Koay2009] Koay C.G., E. Ozarslan, C. Pierpaoli. Probabilistic
              Identification and Estimation of Noise (PIESNO): A
              self-consistent approach and its applications in MRI.
              JMR, 199(1):94-103, 2009.

.. include:: ../links_names.inc


        
.. admonition:: Example source code

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

