BUAN Bundle Assignment Maps Creation

This example explains how we can use BUAN [1] to create assignment maps on a bundle. Divide bundle into N smaller segments.

First import the necessary modules.

import numpy as np

from dipy.data import fetch_bundle_atlas_hcp842, get_two_hcp842_bundles
from dipy.io.streamline import load_trk
from dipy.stats.analysis import assignment_map
from dipy.viz import actor, window

Download and read data for this tutorial

atlas_file, atlas_folder = fetch_bundle_atlas_hcp842()

Read AF left and CST left bundles from already fetched atlas data to use them as model bundles

model_af_l_file, model_cst_l_file = get_two_hcp842_bundles()

sft_af_l = load_trk(model_af_l_file, reference="same", bbox_valid_check=False)
model_af_l = sft_af_l.streamlines

let’s visualize Arcuate Fasiculus Left (AF_L) bundle before assignment maps

interactive = False

scene = window.Scene()
scene.SetBackground(1, 1, 1)
scene.add(actor.line(model_af_l, fake_tube=True, linewidth=6))
scene.set_camera(
    focal_point=(-18.17281532, -19.55606842, 6.92485857),
    position=(-360.11, -30.46, -40.44),
    view_up=(-0.03, 0.028, 0.89),
)
window.record(scene=scene, out_path="af_l_before_assignment_maps.png", size=(600, 600))
if interactive:
    window.show(scene)

AF_L before assignment maps

Creating 100 bundle assignment maps on AF_L using BUAN [1]

rng = np.random.default_rng()

n = 100
indx = assignment_map(model_af_l, model_af_l, n)
indx = np.array(indx)

colors = [rng.random(3) for si in range(n)]

disks_color = []
for i in range(len(indx)):
    disks_color.append(tuple(colors[indx[i]]))

let’s visualize Arcuate Fasiculus Left (AF_L) bundle after assignment maps

interactive = False

scene = window.Scene()
scene.SetBackground(1, 1, 1)
scene.add(actor.line(model_af_l, fake_tube=True, colors=disks_color, linewidth=6))
scene.set_camera(
    focal_point=(-18.17281532, -19.55606842, 6.92485857),
    position=(-360.11, -30.46, -40.44),
    view_up=(-0.03, 0.028, 0.89),
)
window.record(scene=scene, out_path="af_l_after_assignment_maps.png", size=(600, 600))
if interactive:
    window.show(scene)

AF_L after assignment maps

References

[1] (1,2)

Bramsh Qamar Chandio, Shannon Leigh Risacher, Franco Pestilli, Daniel Bullock, Fang-Cheng Yeh, Serge Koudoro, Ariel Rokem, Jaroslaw Harezlak, and Eleftherios Garyfallidis. Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Scientific Reports, 10:17149, October 2020. URL: https://doi.org/10.1038/s41598-020-74054-4, doi:10.1038/s41598-020-74054-4.