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
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output_types
¶ Output connectome format
- Type
[‘gPickle’, ‘mat’, ‘graphml’]
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connectivity_metrics
¶ Set of connectome maps to compute
- Type
[‘Fiber number’, ‘Fiber length’, ‘Fiber density’, ‘Fiber proportion’, ‘Normalized fiber density’, ‘ADC’, ‘gFA’]
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log_visualization
¶ Log visualization that might be obsolete as this has been detached after creation of the bidsappmanager (Default: True)
- Type
traits.Bool
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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
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subject
¶ BIDS subject ID (in the form
sub-XX
)- Type
traits.Str
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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
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create_workflow
(flow, inputnode, outputnode)[source]¶ Create the stage worflow.
- 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
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