""" ======================================== Surface seeding for tractography ======================================== Surface seeding is a way to generate initial position for tractography from cortical surfaces position [Stonge2018]_. """ import numpy as np from dipy.viz import window, actor from dipy.data import get_fnames from dipy.tracking.mesh import (random_coordinates_from_surface, seeds_from_surface_coordinates) from fury.io import load_polydata from fury.utils import (get_polydata_triangles, get_polydata_vertices, get_actor_from_polydata, normals_from_v_f) """ Fetch and load a surface """ brain_lh = get_fnames("fury_surface") polydata = load_polydata(brain_lh) """ Extract the triangles and vertices """ triangles = get_polydata_triangles(polydata) vts = get_polydata_vertices(polydata) """ Display the surface =============================================== First, create an actor from the polydata, to display in the scene """ scene = window.Scene() surface_actor = get_actor_from_polydata(polydata) scene.add(surface_actor) scene.set_camera(position=(-500, 0, 0), view_up=(0.0, 0.0, 1)) # Uncomment the line below to show to display the window # window.show(scene, size=(600, 600), reset_camera=False) window.record(scene, out_path='surface_seed1.png', size=(600, 600)) """ .. figure:: surface_seed1.png :align: center **Initial cortical surface** Generate a list of seeding positions ============================================================== Choose the number of seed """ nb_seeds = 100000 nb_triangles = len(triangles) """ Get a list of triangles indices and trilinear coordinates for each seed """ tri_idx, trilin_co = random_coordinates_from_surface(nb_triangles, nb_seeds) """ Get the 3d cartesian position from triangles indices and trilinear coordinates """ seed_pts = seeds_from_surface_coordinates(triangles, vts, tri_idx, trilin_co) """ Compute normal and get the normal direction for each seeds """ normals = normals_from_v_f(vts, triangles) seed_n = seeds_from_surface_coordinates(triangles, normals, tri_idx, trilin_co) """ Create dot actor for seeds (blue) """ seed_actors = actor.dots(seed_pts, color=(0, 0, 1), dot_size=4.0) """ Create line actors for seeds normals (green outside, red inside) """ normal_length = 0.5 normal_in = np.tile(seed_pts[:, np.newaxis, :], (1, 2, 1)) normal_out = np.tile(seed_pts[:, np.newaxis, :], (1, 2, 1)) normal_in[:, 0] -= seed_n * normal_length normal_out[:, 1] += seed_n * normal_length normal_in_actor = actor.line(normal_in, colors=(1, 0, 0)) normal_out_actor = actor.line(normal_out, colors=(0, 1, 0)) """ Visualise seeds and normals along the surface """ scene = window.Scene() scene.add(surface_actor) scene.add(seed_actors) scene.add(normal_in_actor) scene.add(normal_out_actor) scene.set_camera(position=(-500, 0, 0), view_up=(0.0, 0.0, 1)) # Uncomment the line below to show to display the window # window.show(scene, size=(600, 600), reset_camera=False) window.record(scene, out_path='surface_seed2.png', size=(600, 600)) """ .. figure:: surface_seed2.png :align: center **Surface seeds with normal orientation** References ---------- .. [Stonge2018] St-Onge, E., Daducci, A., Girard, G., & Descoteaux, M. Surface-enhanced tractography (SET). NeuroImage, 169, 524-539, 2018. .. include:: ../links_names.inc """