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