BUAN Bundle Assignment Maps Creation

BUAN Bundle Assignment Maps Creation

This example explains how we can use BUAN [Chandio2020] 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 get_two_hcp842_bundles
from dipy.data import fetch_bundle_atlas_hcp842
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, "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, out_path='af_l_before_assignment_maps.png',
              size=(600, 600))
if interactive:
    window.show(scene)
../../_images/af_l_before_assignment_maps.png

AF_L before assignment maps

Creating 100 bundle assignment maps on AF_L using BUAN [Chandio2020]

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

colors = [np.random.rand(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, out_path='af_l_after_assignment_maps.png',
              size=(600, 600))
if interactive:
    window.show(scene)
../../_images/af_l_after_assignment_maps.png

AF_L after assignment maps

References

[Chandio2020] (1,2)

Chandio, B.Q., Risacher, S.L., Pestilli, F., Bullock, D., Yeh, FC., Koudoro, S., Rokem, A., Harezlak, J., and Garyfallidis, E. Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Sci Rep 10, 17149 (2020)

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.