cmp.stages.connectome.fmri_connectome module¶
Definition of config and stage classes for building functional connectivity matrices.
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class
cmp.stages.connectome.fmri_connectome.ConnectomeConfig[source]¶ Bases:
traits.has_traits.HasTraitsClass used to store configuration parameters of a
ConnectomeStageinstance.-
apply_scrubbing¶ Apply scrubbing before mapping the functional connectome if True (Default: False)
- Type
traits.Bool
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FD_thr¶ Framewise displacement threshold (Default: 0.2)
- Type
traits.Float
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DVARS_thr¶ DVARS (RMS of variance over voxels) threshold (Default: 4.0)
- Type
traits.Float
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output_types¶ Output connectome format
- Type
[‘gPickle’, ‘mat’, ‘cff’, ‘graphml’]
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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.fmri_connectome.ConnectomeStage(bids_dir, output_dir)[source]¶ Bases:
cmp.stages.common.StageClass that represents the connectome building stage of a
fMRIPipeline.-
create_workflow()[source]¶ Create the workflow of the fMRI
ConnectomeStage
See also
cmp.pipelines.functional.fMRI.fMRIPipeline,cmp.stages.connectome.fmri_connectome.ConnectomeConfig-
create_workflow(flow, inputnode, outputnode)[source]¶ Create the stage worflow.
- Parameters
flow (nipype.pipeline.engine.Workflow) – The nipype.pipeline.engine.Workflow instance of the fMRI 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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