"""
==================================================================
Patch2Self: Self-Supervised Denoising via Statistical Independence
==================================================================
Patch2Self [Fadnavis20]_ is a self-supervised learning method for denoising
DWI data, which uses the entire volume to learn a full-rank locally linear
denoiser for that volume. By taking advantage of the oversampled q-space of DWI
data, Patch2Self can separate structure from noise without requiring an
explicit model for either.
Classical denoising algorithms such as Local PCA [Manjon2013]_, [Veraa2016a]_,
Non-local Means [Coupe08]_, Total Variation Norm [Knoll11]_, etc. assume
certain properties on the signal structure. Patch2Self *does not* make any such
assumption on the signal, instead using the fact that the noise across
different 3D volumes of the DWI signal originates from random fluctuations in
the acquired signal.
Since Patch2Self only relies on the randomness of the noise, it can be applied
at any step in the pre-processing pipeline. The design of Patch2Self is such
that it can work on any type of diffusion data/ any body part without
requiring a noise estimation or assumptions on the type of noise (such as its
distribution).
The Patch2Self Framework:
.. _patch2self:
.. figure:: https://github.com/dipy/dipy_data/blob/master/Patch2Self_Framework.PNG?raw=true
:scale: 60 %
:align: center
The above figure demonstrates the working of Patch2Self. The idea is to build
a new regressor for denoising each 3D volume of the 4D diffusion data. This is
done in the following 2 phases:
(A) Self-supervised training: First, we extract 3D Patches from all the ānā
volumes and hold out the target volume to denoise. Each patch from the rest of
the ā(n-1)ā volumes predicts the center voxel of the corresponding patch in the
target volume.
This is done by using the self-supervised loss:
:math:`\mathcal{L}\left(\Phi_{J}\right)=\mathbb{E}\left\|\Phi_{J}\left(Y_{*, *,-j}\right)-Y_{*, 0, j}\right\|^{2}`
(B) Prediction: The same 'n-1' volumes which were used in the training are now
fed into the regressor :math:`\Phi` built in phase (A). The prediction is a
denoised version of held-out volume.
Note: The volume to be denoised is merely used as the target in the training
phase. But is not used in the training set for (A) nor is used to predict the
denoised output in (B).
Let's load the necessary modules:
"""
import numpy as np
from dipy.data import get_fnames
from dipy.io.image import load_nifti, save_nifti
import matplotlib.pyplot as plt
from dipy.denoise.patch2self import patch2self
"""
Now let's load an example dataset and denoise it with Patch2Self. Patch2Self
does not require noise estimation and should work with any kind of diffusion
data.
"""
hardi_fname, hardi_bval_fname, hardi_bvec_fname = get_fnames('stanford_hardi')
data, affine = load_nifti(hardi_fname)
bvals = np.loadtxt(hardi_bval_fname)
denoised_arr = patch2self(data, bvals, model='ols', shift_intensity=True,
clip_negative_vals=False, b0_threshold=50)
"""
The above parameters should give optimal denoising performance for Patch2Self.
The ordinary least squares regression (model='ols') tends to be a little slower
depending on the size of the data. In that case, please consider switching to
ridge regression (model='ridge').
Please do note that sometimes using ridge regression can hamper the
performance of Patch2Self. If so, please use model='ols'.
The array `denoised_arr` contains the denoised output obtained from Patch2Self.
*Note:* Depending on the acquisition, b0 may exhibit signal attenuation or
other artefacts that are not ideal for any denoising algorithm. We therefore
provide an option to skip denoising b0 volumes in the data. This can be done
by using the option `b0_denoising=False` within Patch2Self.
Please set `shift_intensity=True` and `clip_negative_vals=False` by default to
avoid negative values in the denoised output.
The `b0_threshold` is used to separate the b0 volumes from the DWI volumes.
Changing the value of the b0 threshold is needed if the b0 volumes in the
`bval` file have a value greater than the default `b0_threshold`.
The default value of `b0_threshold` in DIPY is set to 50. If using data
such as HCP 7T, the b0 volumes tend to have a higher b-value (>=50)
associated with them in the `bval` file. Please check the b-values for b0s and
adjust the `b0_threshold` accordingly.
Now let's visualize the output and the residuals obtained from the denoising.
"""
# Gets the center slice and the middle volume of the 4D diffusion data.
sli = data.shape[2] // 2
gra = 60 # pick out a random volume for a particular gradient direction
orig = data[:, :, sli, gra]
den = denoised_arr[:, :, sli, gra]
# computes the residuals
rms_diff = np.sqrt((orig - den) ** 2)
fig1, ax = plt.subplots(1, 3, figsize=(12, 6),
subplot_kw={'xticks': [], 'yticks': []})
fig1.subplots_adjust(hspace=0.3, wspace=0.05)
ax.flat[0].imshow(orig.T, cmap='gray', interpolation='none',
origin='lower')
ax.flat[0].set_title('Original')
ax.flat[1].imshow(den.T, cmap='gray', interpolation='none',
origin='lower')
ax.flat[1].set_title('Denoised Output')
ax.flat[2].imshow(rms_diff.T, cmap='gray', interpolation='none',
origin='lower')
ax.flat[2].set_title('Residuals')
fig1.savefig('denoised_patch2self.png')
print("The result saved in denoised_patch2self.png")
"""
.. figure:: denoised_patch2self.png
:align: center
Patch2Self preserved anatomical detail. This can be visually verified by
inspecting the residuals obtained above. Since we do not see any structure in
the difference residuals, it is clear that it preserved the underlying signal
structure and got rid of the stochastic noise.
Below we show how the denoised data can be saved.
"""
save_nifti('denoised_patch2self.nii.gz', denoised_arr, affine)
print("Entire denoised data saved in denoised_patch2self.nii.gz")
"""
Lastly, one can also use Patch2Self in batches if the number of gradient
directions is very high (>=200 volumes). For instance, if the data has 300
volumes, one can split the data into 2 batches, (150 directions each) and still
get the same denoising performance. One can simply run Patch2Self using::
denoised_batch1 = patch2self(data[..., :150], bvals[:150])
denoised_batch2 = patch2self(data[..., 150:], bvals[150:])
After doing this, the 2 denoised batches can be merged as follows::
denoised_p2s = np.concatenate((denoised_batch1, denoised_batch2), axis=3)
One can also consider using the above batching approach to denoise each
shell separately if working with multi-shell data.
References
----------
.. [Fadnavis20] S. Fadnavis, J. Batson, E. Garyfallidis, Patch2Self:
Denoising Diffusion MRI with Self-supervised Learning,
Advances in Neural Information Processing Systems 33 (2020)
.. [Manjon2013] Manjon JV, Coupe P, Concha L, Buades A, Collins DL "Diffusion
Weighted Image Denoising Using Overcomplete Local PCA" (2013).
PLoS ONE 8(9): e73021. doi:10.1371/journal.pone.0073021.
.. [Veraa2016a] Veraart J, Fieremans E, Novikov DS. 2016. Diffusion MRI noise
mapping using random matrix theory. Magnetic Resonance in
Medicine. doi: 10.1002/mrm.26059.
.. [Coupe08] P. Coupe, P. Yger, S. Prima, P. Hellier, C. Kervrann, C.
Barillot, An Optimized Blockwise Non Local Means Denoising
Filter for 3D Magnetic Resonance Images, IEEE Transactions on
Medical Imaging, 27(4):425-441, 2008
.. [Knoll11] F. Knoll, K. Bredies, T. Pock, R. Stollberger, Second order total
generalized variation (TGV) for MRI. Magnetic resonance in
medicine, 65(2), pp.480-491.
.. include:: ../links_names.inc
"""