cmp.stages.connectome.fmri_connectome module¶
Definition of config and stage classes for building functional connectivity matrices.
-
class
cmp.stages.connectome.fmri_connectome.
ConnectomeConfig
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
ConnectomeStage
instance.-
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
-
DVARS_thr
¶ DVARS (RMS of variance over voxels) threshold (Default: 4.0)
- Type
traits.Float
-
output_types
¶ Output connectome format
- Type
[‘gPickle’, ‘mat’, ‘cff’, ‘graphml’]
-
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
-
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.Stage
Class 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
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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 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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