cmp.stages.connectome.connectome module

Definition of config and stage classes for building structural connectivity matrices.

class cmp.stages.connectome.connectome.ConnectomeConfig[source]

Bases: traits.has_traits.HasTraits

Class used to store configuration parameters of a ConnectomeStage instance.

compute_curvature

Compute fiber curvature (Default: False)

Type

traits.Bool

output_types

Output connectome format

Type

[‘gpickle’, ‘mat’, ‘graphml’]

connectivity_metrics

Set of connectome maps to compute

Type

[‘Fiber number’, ‘Fiber length’, ‘Fiber density’, ‘Fiber proportion’, ‘Normalized fiber density’, ‘ADC’, ‘gFA’]

log_visualization

Log visualization that might be obsolete as this has been detached after creation of the bidsappmanager (Default: True)

Type

traits.Bool

circular_layout

Visualization of the connectivity matrix using a circular layout that might be obsolete as this has been detached after creation of the bidsappmanager (Default: False)

Type

traits.Bool

subject

BIDS subject ID (in the form sub-XX)

Type

traits.Str

class cmp.stages.connectome.connectome.ConnectomeStage(bids_dir, output_dir)[source]

Bases: cmp.stages.common.Stage

Class that represents the connectome building stage of a DiffusionPipeline.

create_workflow()[source]

Create the workflow of the diffusion ConnectomeStage

See also

cmp.pipelines.diffusion.diffusion.DiffusionPipeline, cmp.stages.connectome.connectome.ConnectomeConfig

create_workflow(flow, inputnode, outputnode)[source]

Create the stage workflow.

Parameters
  • flow (nipype.pipeline.engine.Workflow) – The nipype.pipeline.engine.Workflow instance of the Diffusion pipeline

  • inputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the inputs of the stage

  • outputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the outputs of the stage

define_inspect_outputs()[source]

Update the inspect_outputs class attribute.

It contains a dictionary of stage outputs with corresponding commands for visual inspection.