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"""
=================================================
An introduction to the Deterministic Tractography
=================================================
Deterministic tractography follows
the trajectory of the most probable pathway within the tracking constraint
(e.g. max angle). It follows the direction with the highest
probability from a distribution, as opposed to the probabilistic tractography
which draws the direction from the distribution. Therefore,
deterministic tractography is equivalent to the probabilistic tractography
returning always the maximum value of the distribution.
Deterministic tractography is an alternative to EuDX deterministic
tractography and unlike EuDX does not follow the peaks of the local models but
uses the entire orientation distributions.
This example is an extension of the
:ref:`sphx_glr_examples_built_fiber_tracking_tracking_probabilistic.py`
example. We begin by loading the data, fitting a Constrained Spherical
Deconvolution (CSD) reconstruction model for the tractography and fitting
the constant solid angle (CSA) reconstruction model to define the tracking
mask (stopping criterion).
"""
from dipy.core.gradients import gradient_table
from dipy.data import default_sphere, get_fnames
from dipy.io.gradients import read_bvals_bvecs
from dipy.io.image import load_nifti, load_nifti_data
from dipy.io.stateful_tractogram import Space, StatefulTractogram
from dipy.io.streamline import save_trk
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel, auto_response_ssst
from dipy.tracking.stopping_criterion import BinaryStoppingCriterion
from dipy.tracking.streamline import Streamlines
from dipy.tracking.tracker import deterministic_tracking
from dipy.tracking.utils import seeds_from_mask
from dipy.viz import actor, colormap, has_fury, window
# Enables/disables interactive visualization
interactive = False
hardi_fname, hardi_bval_fname, hardi_bvec_fname = get_fnames(name="stanford_hardi")
label_fname = get_fnames(name="stanford_labels")
data, affine, hardi_img = load_nifti(hardi_fname, return_img=True)
labels = load_nifti_data(label_fname)
bvals, bvecs = read_bvals_bvecs(hardi_bval_fname, hardi_bvec_fname)
gtab = gradient_table(bvals, bvecs=bvecs)
seed_mask = labels == 2
seeds = seeds_from_mask(seed_mask, affine, density=2)
white_matter = (labels == 1) | (labels == 2)
sc = BinaryStoppingCriterion(white_matter)
response, ratio = auto_response_ssst(gtab, data, roi_radii=10, fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order_max=6)
csd_fit = csd_model.fit(data, mask=white_matter)
###############################################################################
# The Fiber Orientation Distribution (FOD) of the CSD model estimates the
# distribution of small fiber bundles within each voxel. This distribution
# can be used for deterministic fiber tracking. As for probabilistic tracking,
# there are many ways to provide those distributions to the deterministic
# tractography. Here, the spherical harmonic representation of
# the FOD is used.
streamline_generator = deterministic_tracking(
seeds,
sc,
affine,
sh=csd_fit.shm_coeff,
random_seed=1,
sphere=default_sphere,
max_angle=30,
step_size=0.5,
)
streamlines = Streamlines(streamline_generator)
sft = StatefulTractogram(streamlines, hardi_img, Space.RASMM)
save_trk(sft, "tractogram_deterministic.trk")
if has_fury:
scene = window.Scene()
scene.add(actor.line(streamlines, colors=colormap.line_colors(streamlines)))
window.record(scene=scene, out_path="tractogram_deterministic.png", size=(800, 800))
if interactive:
window.show(scene)
###############################################################################
# .. rst-class:: centered small fst-italic fw-semibold
#
# Corpus Callosum using deterministic maximum direction getter
|
