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
- 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
- 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.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
- 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