def run(self,
streamline_files,
model_bundle_files,
greater_than=50,
less_than=1000000,
no_slr=False,
clust_thr=15.,
reduction_thr=15.,
reduction_distance='mdf',
model_clust_thr=2.5,
pruning_thr=8.,
pruning_distance='mdf',
slr_metric='symmetric',
slr_transform='similarity',
slr_matrix='small',
refine=False,
r_reduction_thr=12.,
r_pruning_thr=6.,
no_r_slr=False,
out_dir='',
out_recognized_transf='recognized.trk',
out_recognized_labels='labels.npy'):
""" Recognize bundles
Parameters
----------
streamline_files : string
The path of streamline files where you want to recognize bundles
model_bundle_files : string
The path of model bundle files
greater_than : int, optional
Keep streamlines that have length greater than
this value (default 50) in mm.
less_than : int, optional
Keep streamlines have length less than this value
(default 1000000) in mm.
no_slr : bool, optional
Don't enable local Streamline-based Linear
Registration (default False).
clust_thr : float, optional
MDF distance threshold for all streamlines (default 15)
reduction_thr : float, optional
Reduce search space by (mm) (default 15)
reduction_distance : string, optional
Reduction distance type can be mdf or mam (default mdf)
model_clust_thr : float, optional
MDF distance threshold for the model bundles (default 2.5)
pruning_thr : float, optional
Pruning after matching (default 8).
pruning_distance : string, optional
Pruning distance type can be mdf or mam (default mdf)
slr_metric : string, optional
Options are None, symmetric, asymmetric or diagonal
(default symmetric).
slr_transform : string, optional
Transformation allowed. translation, rigid, similarity or scaling
(Default 'similarity').
slr_matrix : string, optional
Options are 'nano', 'tiny', 'small', 'medium', 'large', 'huge'
(default 'small')
refine : bool, optional
Enable refine recognized bunle (default False)
r_reduction_thr : float, optional
Refine reduce search space by (mm) (default 12)
r_pruning_thr : float, optional
Refine pruning after matching (default 6).
no_r_slr : bool, optional
Don't enable Refine local Streamline-based Linear
Registration (default False).
out_dir : string, optional
Output directory (default input file directory)
out_recognized_transf : string, optional
Recognized bundle in the space of the model bundle
(default 'recognized.trk')
out_recognized_labels : string, optional
Indices of recognized bundle in the original tractogram
(default 'labels.npy')
References
----------
.. [Garyfallidis17] Garyfallidis et al. Recognition of white matter
bundles using local and global streamline-based registration and
clustering, Neuroimage, 2017.
"""
slr = not no_slr
r_slr = not no_r_slr
bounds = [(-30, 30), (-30, 30), (-30, 30), (-45, 45), (-45, 45),
(-45, 45), (0.8, 1.2), (0.8, 1.2), (0.8, 1.2)]
slr_matrix = slr_matrix.lower()
if slr_matrix == 'nano':
slr_select = (100, 100)
if slr_matrix == 'tiny':
slr_select = (250, 250)
if slr_matrix == 'small':
slr_select = (400, 400)
if slr_matrix == 'medium':
slr_select = (600, 600)
if slr_matrix == 'large':
slr_select = (800, 800)
if slr_matrix == 'huge':
slr_select = (1200, 1200)
slr_transform = slr_transform.lower()
if slr_transform == 'translation':
bounds = bounds[:3]
if slr_transform == 'rigid':
bounds = bounds[:6]
if slr_transform == 'similarity':
bounds = bounds[:7]
if slr_transform == 'scaling':
bounds = bounds[:9]
logging.info('### RecoBundles ###')
io_it = self.get_io_iterator()
t = time()
logging.info(streamline_files)
input_obj = nib.streamlines.load(streamline_files)
streamlines = input_obj.streamlines
logging.info(' Loading time %0.3f sec' % (time() - t, ))
rb = RecoBundles(streamlines,
greater_than=greater_than,
less_than=less_than)
for _, mb, out_rec, out_labels in io_it:
t = time()
logging.info(mb)
model_bundle = nib.streamlines.load(mb).streamlines
logging.info(' Loading time %0.3f sec' % (time() - t, ))
logging.info("model file = ")
logging.info(mb)
recognized_bundle, labels = \
rb.recognize(
model_bundle,
model_clust_thr=model_clust_thr,
reduction_thr=reduction_thr,
reduction_distance=reduction_distance,
pruning_thr=pruning_thr,
pruning_distance=pruning_distance,
slr=slr,
slr_metric=slr_metric,
slr_x0=slr_transform,
slr_bounds=bounds,
slr_select=slr_select,
slr_method='L-BFGS-B')
if refine:
if len(recognized_bundle) > 1:
# affine
x0 = np.array([0, 0, 0, 0, 0, 0, 1., 1., 1, 0, 0, 0])
affine_bounds = [(-30, 30), (-30, 30), (-30, 30),
(-45, 45), (-45, 45), (-45, 45),
(0.8, 1.2), (0.8, 1.2), (0.8, 1.2),
(-10, 10), (-10, 10), (-10, 10)]
recognized_bundle, labels = \
rb.refine(
model_bundle,
recognized_bundle,
model_clust_thr=model_clust_thr,
reduction_thr=r_reduction_thr,
reduction_distance=reduction_distance,
pruning_thr=r_pruning_thr,
pruning_distance=pruning_distance,
slr=r_slr,
slr_metric=slr_metric,
slr_x0=x0,
slr_bounds=affine_bounds,
slr_select=slr_select,
slr_method='L-BFGS-B')
if len(labels) > 0:
ba, bmd = rb.evaluate_results(model_bundle, recognized_bundle,
slr_select)
logging.info("Bundle adjacency Metric {0}".format(ba))
logging.info("Bundle Min Distance Metric {0}".format(bmd))
new_tractogram = nib.streamlines.Tractogram(
recognized_bundle, affine_to_rasmm=np.eye(4))
nib.streamlines.save(new_tractogram,
out_rec,
header=input_obj.header)
logging.info('Saving output files ...')
np.save(out_labels, np.array(labels))
logging.info(out_rec)
logging.info(out_labels)
def run(self,
streamline_files,
model_bundle_files,
greater_than=50,
less_than=1000000,
no_slr=False,
clust_thr=15.,
reduction_thr=15.,
reduction_distance='mdf',
model_clust_thr=2.5,
pruning_thr=8.,
pruning_distance='mdf',
slr_metric='symmetric',
slr_transform='similarity',
slr_matrix='small',
refine=False,
r_reduction_thr=12.,
r_pruning_thr=6.,
no_r_slr=False,
out_dir='',
out_recognized_transf='recognized.trk',
out_recognized_labels='labels.npy'):
""" Recognize bundles
Parameters
----------
streamline_files : string
The path of streamline files where you want to recognize bundles.
model_bundle_files : string
The path of model bundle files.
greater_than : int, optional
Keep streamlines that have length greater than
this value in mm.
less_than : int, optional
Keep streamlines have length less than this value
in mm.
no_slr : bool, optional
Don't enable local Streamline-based Linear
Registration.
clust_thr : float, optional
MDF distance threshold for all streamlines.
reduction_thr : float, optional
Reduce search space by (mm).
reduction_distance : string, optional
Reduction distance type can be mdf or mam.
model_clust_thr : float, optional
MDF distance threshold for the model bundles.
pruning_thr : float, optional
Pruning after matching.
pruning_distance : string, optional
Pruning distance type can be mdf or mam.
slr_metric : string, optional
Options are None, symmetric, asymmetric or diagonal.
slr_transform : string, optional
Transformation allowed. translation, rigid, similarity or scaling.
slr_matrix : string, optional
Options are 'nano', 'tiny', 'small', 'medium', 'large', 'huge'.
refine : bool, optional
Enable refine recognized bundle.
r_reduction_thr : float, optional
Refine reduce search space by (mm).
r_pruning_thr : float, optional
Refine pruning after matching.
no_r_slr : bool, optional
Don't enable Refine local Streamline-based Linear
Registration.
out_dir : string, optional
Output directory. (default current directory)
out_recognized_transf : string, optional
Recognized bundle in the space of the model bundle.
out_recognized_labels : string, optional
Indices of recognized bundle in the original tractogram.
References
----------
.. [Garyfallidis17] Garyfallidis et al. Recognition of white matter
bundles using local and global streamline-based registration and
clustering, Neuroimage, 2017.
.. [Chandio2020] 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)
"""
slr = not no_slr
r_slr = not no_r_slr
bounds = [(-30, 30), (-30, 30), (-30, 30), (-45, 45), (-45, 45),
(-45, 45), (0.8, 1.2), (0.8, 1.2), (0.8, 1.2)]
slr_matrix = slr_matrix.lower()
if slr_matrix == 'nano':
slr_select = (100, 100)
if slr_matrix == 'tiny':
slr_select = (250, 250)
if slr_matrix == 'small':
slr_select = (400, 400)
if slr_matrix == 'medium':
slr_select = (600, 600)
if slr_matrix == 'large':
slr_select = (800, 800)
if slr_matrix == 'huge':
slr_select = (1200, 1200)
slr_transform = slr_transform.lower()
if slr_transform == 'translation':
bounds = bounds[:3]
if slr_transform == 'rigid':
bounds = bounds[:6]
if slr_transform == 'similarity':
bounds = bounds[:7]
if slr_transform == 'scaling':
bounds = bounds[:9]
logging.info('### RecoBundles ###')
io_it = self.get_io_iterator()
t = time()
logging.info(streamline_files)
input_obj = load_tractogram(streamline_files,
'same',
bbox_valid_check=False)
streamlines = input_obj.streamlines
logging.info(' Loading time %0.3f sec' % (time() - t, ))
rb = RecoBundles(streamlines,
greater_than=greater_than,
less_than=less_than)
for _, mb, out_rec, out_labels in io_it:
t = time()
logging.info(mb)
model_bundle = load_tractogram(mb, 'same',
bbox_valid_check=False).streamlines
logging.info(' Loading time %0.3f sec' % (time() - t, ))
logging.info("model file = ")
logging.info(mb)
recognized_bundle, labels = \
rb.recognize(
model_bundle,
model_clust_thr=model_clust_thr,
reduction_thr=reduction_thr,
reduction_distance=reduction_distance,
pruning_thr=pruning_thr,
pruning_distance=pruning_distance,
slr=slr,
slr_metric=slr_metric,
slr_x0=slr_transform,
slr_bounds=bounds,
slr_select=slr_select,
slr_method='L-BFGS-B')
if refine:
if len(recognized_bundle) > 1:
# affine
x0 = np.array([0, 0, 0, 0, 0, 0, 1., 1., 1, 0, 0, 0])
affine_bounds = [(-30, 30), (-30, 30), (-30, 30),
(-45, 45), (-45, 45), (-45, 45),
(0.8, 1.2), (0.8, 1.2), (0.8, 1.2),
(-10, 10), (-10, 10), (-10, 10)]
recognized_bundle, labels = \
rb.refine(
model_bundle,
recognized_bundle,
model_clust_thr=model_clust_thr,
reduction_thr=r_reduction_thr,
reduction_distance=reduction_distance,
pruning_thr=r_pruning_thr,
pruning_distance=pruning_distance,
slr=r_slr,
slr_metric=slr_metric,
slr_x0=x0,
slr_bounds=affine_bounds,
slr_select=slr_select,
slr_method='L-BFGS-B')
if len(labels) > 0:
ba, bmd = rb.evaluate_results(model_bundle, recognized_bundle,
slr_select)
logging.info("Bundle adjacency Metric {0}".format(ba))
logging.info("Bundle Min Distance Metric {0}".format(bmd))
new_tractogram = StatefulTractogram(recognized_bundle,
streamline_files, Space.RASMM)
save_tractogram(new_tractogram, out_rec, bbox_valid_check=False)
logging.info('Saving output files ...')
np.save(out_labels, np.array(labels))
logging.info(out_rec)
logging.info(out_labels)
def run(self, streamline_files, model_bundle_files,
greater_than=50, less_than=1000000,
no_slr=False, clust_thr=15.,
reduction_thr=15.,
reduction_distance='mdf',
model_clust_thr=2.5,
pruning_thr=8.,
pruning_distance='mdf',
slr_metric='symmetric',
slr_transform='similarity',
slr_matrix='small',
refine=False, r_reduction_thr=12.,
r_pruning_thr=6., no_r_slr=False,
out_dir='',
out_recognized_transf='recognized.trk',
out_recognized_labels='labels.npy'):
""" Recognize bundles
Parameters
----------
streamline_files : string
The path of streamline files where you want to recognize bundles
model_bundle_files : string
The path of model bundle files
greater_than : int, optional
Keep streamlines that have length greater than
this value (default 50) in mm.
less_than : int, optional
Keep streamlines have length less than this value
(default 1000000) in mm.
no_slr : bool, optional
Don't enable local Streamline-based Linear
Registration (default False).
clust_thr : float, optional
MDF distance threshold for all streamlines (default 15)
reduction_thr : float, optional
Reduce search space by (mm) (default 15)
reduction_distance : string, optional
Reduction distance type can be mdf or mam (default mdf)
model_clust_thr : float, optional
MDF distance threshold for the model bundles (default 2.5)
pruning_thr : float, optional
Pruning after matching (default 8).
pruning_distance : string, optional
Pruning distance type can be mdf or mam (default mdf)
slr_metric : string, optional
Options are None, symmetric, asymmetric or diagonal
(default symmetric).
slr_transform : string, optional
Transformation allowed. translation, rigid, similarity or scaling
(Default 'similarity').
slr_matrix : string, optional
Options are 'nano', 'tiny', 'small', 'medium', 'large', 'huge'
(default 'small')
refine : bool, optional
Enable refine recognized bunle (default False)
r_reduction_thr : float, optional
Refine reduce search space by (mm) (default 12)
r_pruning_thr : float, optional
Refine pruning after matching (default 6).
no_r_slr : bool, optional
Don't enable Refine local Streamline-based Linear
Registration (default False).
out_dir : string, optional
Output directory (default input file directory)
out_recognized_transf : string, optional
Recognized bundle in the space of the model bundle
(default 'recognized.trk')
out_recognized_labels : string, optional
Indices of recognized bundle in the original tractogram
(default 'labels.npy')
References
----------
.. [Garyfallidis17] Garyfallidis et al. Recognition of white matter
bundles using local and global streamline-based registration and
clustering, Neuroimage, 2017.
"""
slr = not no_slr
r_slr = not no_r_slr
bounds = [(-30, 30), (-30, 30), (-30, 30),
(-45, 45), (-45, 45), (-45, 45),
(0.8, 1.2), (0.8, 1.2), (0.8, 1.2)]
slr_matrix = slr_matrix.lower()
if slr_matrix == 'nano':
slr_select = (100, 100)
if slr_matrix == 'tiny':
slr_select = (250, 250)
if slr_matrix == 'small':
slr_select = (400, 400)
if slr_matrix == 'medium':
slr_select = (600, 600)
if slr_matrix == 'large':
slr_select = (800, 800)
if slr_matrix == 'huge':
slr_select = (1200, 1200)
slr_transform = slr_transform.lower()
if slr_transform == 'translation':
bounds = bounds[:3]
if slr_transform == 'rigid':
bounds = bounds[:6]
if slr_transform == 'similarity':
bounds = bounds[:7]
if slr_transform == 'scaling':
bounds = bounds[:9]
logging.info('### RecoBundles ###')
io_it = self.get_io_iterator()
t = time()
logging.info(streamline_files)
streamlines, header = load_trk(streamline_files)
logging.info(' Loading time %0.3f sec' % (time() - t,))
rb = RecoBundles(streamlines, greater_than=greater_than,
less_than=less_than)
for _, mb, out_rec, out_labels in io_it:
t = time()
logging.info(mb)
model_bundle, _ = load_trk(mb)
logging.info(' Loading time %0.3f sec' % (time() - t,))
logging.info("model file = ")
logging.info(mb)
recognized_bundle, labels = \
rb.recognize(
model_bundle,
model_clust_thr=model_clust_thr,
reduction_thr=reduction_thr,
reduction_distance=reduction_distance,
pruning_thr=pruning_thr,
pruning_distance=pruning_distance,
slr=slr,
slr_metric=slr_metric,
slr_x0=slr_transform,
slr_bounds=bounds,
slr_select=slr_select,
slr_method='L-BFGS-B')
if refine:
if len(recognized_bundle) > 1:
# affine
x0 = np.array([0, 0, 0, 0, 0, 0, 1., 1., 1, 0, 0, 0])
affine_bounds = [(-30, 30), (-30, 30), (-30, 30),
(-45, 45), (-45, 45), (-45, 45),
(0.8, 1.2), (0.8, 1.2), (0.8, 1.2),
(-10, 10), (-10, 10), (-10, 10)]
recognized_bundle, labels = \
rb.refine(
model_bundle,
recognized_bundle,
model_clust_thr=model_clust_thr,
reduction_thr=r_reduction_thr,
reduction_distance=reduction_distance,
pruning_thr=r_pruning_thr,
pruning_distance=pruning_distance,
slr=r_slr,
slr_metric=slr_metric,
slr_x0=x0,
slr_bounds=affine_bounds,
slr_select=slr_select,
slr_method='L-BFGS-B')
if len(labels) > 0:
ba, bmd = rb.evaluate_results(
model_bundle, recognized_bundle,
slr_select)
logging.info("Bundle adjacency Metric {0}".format(ba))
logging.info("Bundle Min Distance Metric {0}".format(bmd))
save_trk(out_rec, recognized_bundle, np.eye(4))
logging.info('Saving output files ...')
np.save(out_labels, np.array(labels))
logging.info(out_rec)
logging.info(out_labels)
