Bootstrap and Closest Peak Direction Getters Example

This example shows how choices in direction-getter impact fiber tracking results by demonstrating the bootstrap direction getter (a type of probabilistic tracking, as described in Berman et al. (2008) [Berman2008] a nd the closest peak direction getter (a type of deterministic tracking). (Amirbekian, PhD thesis, 2016)

This example is an extension of the Introduction to Basic Tracking example. Let’s start by loading the necessary modules for executing this tutorial.

# Enables/disables interactive visualization
interactive = False

from dipy.data import read_stanford_labels, small_sphere
from dipy.direction import BootDirectionGetter, ClosestPeakDirectionGetter
from dipy.io.stateful_tractogram import Space, StatefulTractogram
from dipy.io.streamline import save_trk
from dipy.reconst.csdeconv import (ConstrainedSphericalDeconvModel,
                                   auto_response)
from dipy.reconst.shm import CsaOdfModel
from dipy.tracking import utils
from dipy.tracking.local_tracking import LocalTracking
from dipy.tracking.streamline import Streamlines
from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion
from dipy.viz import window, actor, colormap, has_fury


hardi_img, gtab, labels_img = read_stanford_labels()
data = hardi_img.get_data()
labels = labels_img.get_data()
affine = hardi_img.affine

seed_mask = (labels == 2)
white_matter = (labels == 1) | (labels == 2)
seeds = utils.seeds_from_mask(seed_mask, affine, density=1)

Next, we fit the CSD model.

response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=6)
csd_fit = csd_model.fit(data, mask=white_matter)

we use the CSA fit to calculate GFA, which will serve as our stopping criterion.

csa_model = CsaOdfModel(gtab, sh_order=6)
gfa = csa_model.fit(data, mask=white_matter).gfa
stopping_criterion = ThresholdStoppingCriterion(gfa, .25)

Next, we need to set up our two direction getters

Example #1: Bootstrap direction getter with CSD Model

boot_dg_csd = BootDirectionGetter.from_data(data, csd_model, max_angle=30.,
                                            sphere=small_sphere)
boot_streamline_generator = LocalTracking(boot_dg_csd, stopping_criterion,
                                          seeds, affine, step_size=.5)
streamlines = Streamlines(boot_streamline_generator)
sft = StatefulTractogram(streamlines, hardi_img, Space.RASMM)
save_trk(sft, "tractogram_bootstrap_dg.trk")

if has_fury:
    r = window.Renderer()
    r.add(actor.line(streamlines, colormap.line_colors(streamlines)))
    window.record(r, out_path='tractogram_bootstrap_dg.png', size=(800, 800))
    if interactive:
        window.show(r)

Corpus Callosum Bootstrap Probabilistic Direction Getter

We have created a bootstrapped probabilistic set of streamlines. If you repeat the fiber tracking (keeping all inputs the same) you will NOT get exactly the same set of streamlines.

Example #2: Closest peak direction getter with CSD Model

pmf = csd_fit.odf(small_sphere).clip(min=0)
peak_dg = ClosestPeakDirectionGetter.from_pmf(pmf, max_angle=30.,
                                              sphere=small_sphere)
peak_streamline_generator = LocalTracking(peak_dg, stopping_criterion, seeds,
                                          affine, step_size=.5)
streamlines = Streamlines(peak_streamline_generator)
sft = StatefulTractogram(streamlines, hardi_img, Space.RASMM)
save_trk(sft, "closest_peak_dg_CSD.trk")

if has_fury:
    r = window.Renderer()
    r.add(actor.line(streamlines, colormap.line_colors(streamlines)))
    window.record(r, out_path='tractogram_closest_peak_dg.png',
                  size=(800, 800))
    if interactive:
        window.show(r)

Corpus Callosum Closest Peak Deterministic Direction Getter

We have created a set of streamlines using the closest peak direction getter, which is a type of deterministic tracking. If you repeat the fiber tracking (keeping all inputs the same) you will get exactly the same set of streamlines.

References

Berman2008

Berman, J. et al., Probabilistic streamline q-ball

tractography using the residual bootstrap, NeuroImage, vol 39, no 1, 2008

Example source code

You can download the full source code of this example. This same script is also included in the dipy source distribution under the doc/examples/ directory.