cmp.stages.diffusion.tracking module

Tracking methods and workflows of the diffusion stage.

class cmp.stages.diffusion.tracking.Dipy_tracking_config

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

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)

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)

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

cmp.stages.diffusion.tracking.get_freesurfer_parcellation(roi_files)

Return the first file in the list of parcellation files

Parameters

roi_files (list of traits.File) – List of parcellation files