cmp.stages.diffusion.tracking module¶
Tracking methods and workflows of the diffusion stage.
-
class
cmp.stages.diffusion.tracking.
Dipy_tracking_config
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store Dipy diffusion reconstruction sub-workflow configuration parameters.
-
imaging_model
¶ Diffusion imaging model (For example ‘DTI’)
- Type
traits.Str
-
tracking_mode
¶ Type of local tractography algorithm (Can be “Deterministic” or “Probabilistic”)
- Type
traits.Str
-
SD
¶ If
True
, inputs are coming from Constrained Spherical Deconvolution reconstruction- Type
traits.Bool
-
number_of_seeds
¶ Number of seeds (Default: 1000)
- Type
traits.Int
-
seed_density
¶ Number of seeds to place along each direction where a density of 2 is the same as [2, 2, 2] and will result in a total of 8 seeds per voxel (Default: 1.0)
- Type
traits.Float
-
fa_thresh
¶ Fractional Anisotropy (FA) threshold (Default: 0.2)
- Type
traits.Float
-
step_size
¶ Tractography algorithm step size (Default: 0.5)
- Type
traits.traits.Float
-
max_angle
¶ Maximum streamline angle allowed (Default: 25.0)
- Type
traits.Float
-
sh_order
¶ Order used for Constrained Spherical Deconvolution reconstruction (Default: 8)
- Type
traits.Int
-
use_act
¶ Use FAST for partial volume estimation and Anatomically-Constrained Tractography (ACT) tissue classifier (Default: False)
- Type
traits.Bool
-
seed_from_gmwmi
¶ Seed from Grey Matter / White Matter interface (requires Anatomically-Constrained Tractography (ACT)) (Default: False)
- Type
traits.Bool
-
-
class
cmp.stages.diffusion.tracking.
MRtrix_tracking_config
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store Dipy diffusion reconstruction sub-workflow configuration parameters.
-
tracking_mode
¶ Type of local tractography algorithm (Can be “Deterministic” or “Probabilistic”)
- Type
traits.Str
-
SD
¶ If
True
, inputs are coming from Constrained Spherical Deconvolution reconstruction- Type
traits.Bool
-
desired_number_of_tracks
¶ Desired number of output streamlines in the tractogram (Default: 1M)
- Type
traits.Int
-
curvature = Float
Maximum streamline curvature (Default: 2.0)
-
min_length = Float
Minimal streamline length (Default: 5)
-
max_length = Float
Maximal streamline length (Default: 500)
-
angle
¶ Maximum streamline angle allowed (Default: 45.0)
- Type
traits.Float
-
cutoff_value
¶ Cut-off value to terminate streamline (Default: 0.05)
- Type
traits.Float
-
use_act
¶ Use
5ttgen
for brain tissue types estimation and Anatomically-Constrained Tractography (ACT) tissue classifier (Default: False)- Type
traits.Bool
-
seed_from_gmwmi
¶ Seed from Grey Matter / White Matter interface (requires Anatomically-Constrained Tractography (ACT)) (Default: False)
- Type
traits.Bool
-
crop_at_gmwmi
¶ Crop streamline endpoints more precisely as they cross the GM-WM interface (requires Anatomically-Constrained Tractography (ACT)) (Default: True)
- Type
traits.Bool
-
backtrack
¶ Allow tracks to be truncated (requires Anatomically-Constrained Tractography (ACT)) (Default: True)
- Type
traits.Bool
-
sift
¶ Filter tractogram using mrtrix3 SIFT (Default: True)
- Type
traits.Bool
-
-
cmp.stages.diffusion.tracking.
create_dipy_tracking_flow
(config)[source]¶ Create the tractography sub-workflow of the
DiffusionStage
using Dipy.- Parameters
config (Dipy_tracking_config) – Sub-workflow configuration object
- Returns
flow – Built tractography sub-workflow
- Return type
nipype.pipeline.engine.Workflow
-
cmp.stages.diffusion.tracking.
create_mrtrix_tracking_flow
(config)[source]¶ Create the tractography sub-workflow of the
DiffusionStage
using MRtrix3.- Parameters
config (MRtrix_tracking_config) – Sub-workflow configuration object
- Returns
flow – Built tractography sub-workflow
- Return type
nipype.pipeline.engine.Workflow