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Tissue Classifier tracking example - changed seeding mask to wm only voxels #851

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Feb 10, 2016
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Tissue Classifier tracking example - changed seeding mask to wm only voxels #851

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25b80b3
RF - changed seeding mask to wm only voxels
gabknight Jan 29, 2016
ee335d4
fixed typo
gabknight Jan 29, 2016
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16 changes: 10 additions & 6 deletions doc/examples/tracking_tissue_classifier.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,16 @@

This example is an extension of the
:ref:`example_deterministic_fiber_tracking` example. We begin by loading the
data, fitting a Constrained Spherical Deconvolution (CSD) reconstruction
data, creating a seeding mask from white matter voxels of the corpus callosum,
fitting a Constrained Spherical Deconvolution (CSD) reconstruction
model and creating the maximum deterministic direction getter.
"""

import numpy as np

from dipy.data import read_stanford_labels, default_sphere
from dipy.data import (read_stanford_labels,
default_sphere,
read_stanford_pve_maps)
from dipy.direction import DeterministicMaximumDirectionGetter
from dipy.io.trackvis import save_trk
from dipy.reconst.csdeconv import (ConstrainedSphericalDeconvModel,
Expand All @@ -37,12 +40,14 @@
ren = fvtk.ren()

hardi_img, gtab, labels_img = read_stanford_labels()
_, _, img_pve_wm = read_stanford_pve_maps()
data = hardi_img.get_data()
labels = labels_img.get_data()
affine = hardi_img.get_affine()
white_matter = img_pve_wm.get_data()

seed_mask = np.logical_and(labels == 2, white_matter == 1)

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

response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
Expand Down Expand Up @@ -154,7 +159,7 @@

from dipy.tracking.local import BinaryTissueClassifier

binary_classifier = BinaryTissueClassifier(white_matter)
binary_classifier = BinaryTissueClassifier(white_matter == 1)

fig = plt.figure()
plt.xticks([])
Expand Down Expand Up @@ -222,7 +227,6 @@
- 'INVALIDPOINT': exclude_map > 0.5.
"""

from dipy.data import read_stanford_pve_maps
from dipy.tracking.local import ActTissueClassifier

img_pve_csf, img_pve_gm, img_pve_wm = read_stanford_pve_maps()
Expand Down