def main():
#set some values to be used later
sh_order = 6
verts, edges, efaces = create_unit_sphere(4)
#read_data from disk
data, fa, bvec, bval, voxel_size = sample_hardi_data()
data_slice = data[32:76, 32:76, 26:27]
fa_slice = fa[32:76, 32:76, 26]
#normalize data by dividing by b0, this is needed so we can take log later
norm_data = normalize_data(data_slice, bval, min_signal=1)
#create an instance of the model
model_instance = MonoExpOpdfModel(sh_order, bval, bvec, .006)
model_instance.set_sampling_points(verts, edges)
#use the model it fit the data
opdfs_sampled_at_verts = model_instance.evaluate(norm_data)
opdfs_sph_harm_coef = model_instance.fit_data(norm_data)
#display the opdf blobs using mayavi
faces = edges[efaces, 0]
show_blobs(opdfs_sampled_at_verts, verts, faces)
mlab.imshow(fa_slice, colormap='gray', interpolate=False)
mlab.show()
def main():
"""Track example dataset"""
data, fa, bvec, bval, voxel_size = sample_hardi_data()
seed_mask, target_mask = sample_tracking_seedNtarget()
density = [1, 1, 2]
start_step = [-0.3, -0.7, -0.7]
tracks = simple_tracking_function(data, fa, bval, bvec, seed_mask,
start_step, voxel_size, density)
tracks = list(tracks)
targeted_tracks = target(tracks, target_mask, voxel_size)
"""
def main():
"""Track example dataset"""
data, fa, bvec, bval, voxel_size = sample_hardi_data()
seed_mask, target_mask = sample_tracking_seedNtarget()
density = [1, 1, 2]
start_step = [-0.3, -0.7, -0.7]
tracks = simple_tracking_function(data, fa, bval, bvec, seed_mask, start_step,
voxel_size, density)
tracks = list(tracks)
targeted_tracks = target(tracks, target_mask, voxel_size)
"""
