This example shows how to use Constrained Spherical Deconvolution (CSD)
introduced by Tournier et al. [Tournier2007]. This method is mainly useful with datasets with gradient directions acquired on
a spherical grid. The basic idea with this method is that if we could estimate the response
function of a single fiber then we could deconvolve the measured signal and
obtain the underlying fiber distribution. In this way, the reconstruction of the fiber orientation distribution function
(fODF) in CSD involves two steps: Estimation of the fiber response function Use the response function to reconstruct the fODF Let’s first load the data. We will use a dataset with 10 b0s and 150 non-b0s
with b-value 2000. You can verify the b-values of the dataset by looking at the attribute
There are many strategies to estimate the fiber response function. Here two
different strategies are presented. Strategy 1 - response function estimates from a local brain region
One simple way to estimate the fiber response function is to look for regions
of the brain where it is known that there are single coherent fiber
populations. For example, if we use a ROI at the center of the brain, we will
find single fibers from the corpus callosum. The Note that the The It is good practice to always validate the result of auto_response_ssst. For
this purpose we can print the elements of (array([ 0.0014, 0.00029, 0.00029]), 416.206) The tensor generated from the response must be prolate (two smaller eigenvalues
should be equal) and look anisotropic with a ratio of second to first
eigenvalue of about 0.2. Or in other words, the axial diffusivity of this
tensor should be around 5 times larger than the radial diffusivity. 0.21197 We can double-check that we have a good response function by visualizing the
response function’s ODF. Here is how you would do that: Strategy 2 - data-driven calibration of response function Depending
on the dataset, FA threshold may not be the best way to find the best possible
response function. For one, it depends on the diffusion tensor
(FA and first eigenvector), which has lower accuracy at high
b-values. Alternatively, the response function can be calibrated in a
data-driven manner [Tax2014]. First, the data is deconvolved with a ‘fat’ response function. All voxels that
are considered to contain only one peak in this deconvolution (as determined by
the peak threshold which gives an upper limit of the ratio of the second peak
to the first peak) are maintained, and from these voxels a new response
function is determined. This process is repeated until convergence is
reached. Here we calibrate the response function on a small part of the data. A WM mask can shorten computation time for the whole dataset. Here it is
created based on the DTI fit. We can check the shape of the signal of the response function, which should be
like a pancake: After estimating a response function for one of the strategies shown above,
we are ready to start the deconvolution process. Let’s import the CSD model
and fit the datasets. For illustration purposes we will fit only a small portion of the data. Show the CSD-based ODFs also known as FODFs (fiber ODFs). Here we visualize only a 30x30 region. In DIPY we also provide tools for finding the peak directions (maxima) of the
ODFs. For this purpose we recommend using We can finally visualize both the ODFs and peaks in the same space. J-D. Tournier, F. Calamante and A. Connelly, “Robust
determination of the fibre orientation distribution in diffusion MRI:
Non-negativity constrained super-resolved spherical deconvolution”,
Neuroimage, vol. 35, no. 4, pp. 1459-1472, 2007. C.M.W. Tax, B. Jeurissen, S.B. Vos, M.A. Viergever, A. Leemans,
“Recursive calibration of the fiber response function for spherical
deconvolution of diffusion MRI data”, Neuroimage, vol. 86, pp. 67-80, 2014. Example source code You can download Reconstruction with Constrained Spherical Deconvolution
import numpy as np
from dipy.core.gradients import gradient_table
from dipy.data import get_fnames, default_sphere
from dipy.io.gradients import read_bvals_bvecs
from dipy.io.image import load_nifti
hardi_fname, hardi_bval_fname, hardi_bvec_fname = get_fnames('stanford_hardi')
data, affine = load_nifti(hardi_fname)
bvals, bvecs = read_bvals_bvecs(hardi_bval_fname, hardi_bvec_fname)
gtab = gradient_table(bvals, bvecs)
gtab.bvals
. Now that a dataset with multiple gradient directions is
loaded, we can proceed with the two steps of CSD.Step 1. Estimation of the fiber response function
auto_response_ssst
function will calculate FA for a cuboid ROI of radii equal to roi_radii
in
the center of the volume and return the response function estimated in that
region for the voxels with FA higher than 0.7.from dipy.reconst.csdeconv import (auto_response_ssst,
mask_for_response_ssst,
response_from_mask_ssst)
response, ratio = auto_response_ssst(gtab, data, roi_radii=10, fa_thr=0.7)
auto_response_ssst
function calls two functions that can be
used separately. First, the function mask_for_response_ssst
creates a mask
of voxels within the cuboid ROI that meet the FA threshold constraint. This
mask can be used to calculate the number of voxels that were kept, or to also
apply an external mask (a WM mask for example). Second, the function
response_from_mask_ssst
takes the mask and returns the response function
calculated within the mask. If no changes are made to the mask between the two
calls, the resulting responses should be identical.mask = mask_for_response_ssst(gtab, data, roi_radii=10, fa_thr=0.7)
nvoxels = np.sum(mask)
print(nvoxels)
response, ratio = response_from_mask_ssst(gtab, data, mask)
response
tuple contains two elements. The first is an array with
the eigenvalues of the response function and the second is the average S0 for
this response.response
and have a look at their
values.print(response)
print(ratio)
from dipy.viz import window, actor
from dipy.sims.voxel import single_tensor_odf
# Enables/disables interactive visualization
interactive = False
scene = window.Scene()
evals = response[0]
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
response_odf = single_tensor_odf(default_sphere.vertices, evals, evecs)
# transform our data from 1D to 4D
response_odf = response_odf[None, None, None, :]
response_actor = actor.odf_slicer(response_odf, sphere=default_sphere,
colormap='plasma')
scene.add(response_actor)
print('Saving illustration as csd_response.png')
window.record(scene, out_path='csd_response.png', size=(200, 200))
if interactive:
window.show(scene)
scene.rm(response_actor)
from dipy.reconst.csdeconv import recursive_response
import dipy.reconst.dti as dti
tenmodel = dti.TensorModel(gtab)
tenfit = tenmodel.fit(data, mask=data[..., 0] > 200)
from dipy.reconst.dti import fractional_anisotropy
FA = fractional_anisotropy(tenfit.evals)
MD = dti.mean_diffusivity(tenfit.evals)
wm_mask = (np.logical_or(FA >= 0.4, (np.logical_and(FA >= 0.15, MD >= 0.0011))))
response = recursive_response(gtab, data, mask=wm_mask, sh_order=8,
peak_thr=0.01, init_fa=0.08,
init_trace=0.0021, iter=8, convergence=0.001,
parallel=True, num_processes=2)
response_signal = response.on_sphere(default_sphere)
# transform our data from 1D to 4D
response_signal = response_signal[None, None, None, :]
response_actor = actor.odf_slicer(response_signal, sphere=default_sphere,
colormap='plasma')
scene = window.Scene()
scene.add(response_actor)
print('Saving illustration as csd_recursive_response.png')
window.record(scene, out_path='csd_recursive_response.png', size=(200, 200))
if interactive:
window.show(scene)
scene.rm(response_actor)
Step 2. fODF reconstruction
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
data_small = data[20:50, 55:85, 38:39]
csd_fit = csd_model.fit(data_small)
csd_odf = csd_fit.odf(default_sphere)
fodf_spheres = actor.odf_slicer(csd_odf, sphere=default_sphere, scale=0.9,
norm=False, colormap='plasma')
scene.add(fodf_spheres)
print('Saving illustration as csd_odfs.png')
window.record(scene, out_path='csd_odfs.png', size=(600, 600))
if interactive:
window.show(scene)
peaks_from_model
.from dipy.direction import peaks_from_model
csd_peaks = peaks_from_model(model=csd_model,
data=data_small,
sphere=default_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True,
num_processes=2)
scene.clear()
fodf_peaks = actor.peak_slicer(csd_peaks.peak_dirs, csd_peaks.peak_values)
scene.add(fodf_peaks)
print('Saving illustration as csd_peaks.png')
window.record(scene, out_path='csd_peaks.png', size=(600, 600))
if interactive:
window.show(scene)
fodf_spheres.GetProperty().SetOpacity(0.4)
scene.add(fodf_spheres)
print('Saving illustration as csd_both.png')
window.record(scene, out_path='csd_both.png', size=(600, 600))
if interactive:
window.show(scene)
References
the full source code of this example
. This same script is also included in the dipy source distribution under the doc/examples/
directory.