cmp.stages.functional.functionalMRI module¶
Definition of config and stage classes for the extra functional preprocessing stage.
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class
cmp.stages.functional.functionalMRI.
FunctionalMRIConfig
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
FunctionalMRIStage
object.-
global_nuisance
¶ Perform global nuisance regression (Default: False)
- Type
traits.Bool
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csf
¶ Perform CSF nuisance regression (Default: True)
- Type
traits.Bool
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wm
¶ Perform White-Matter nuisance regression (Default: True)
- Type
traits.Bool
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motion
¶ Perform motion nuisance regression (Default: True)
- Type
traits.Bool
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detrending = Bool
Perform detrending (Default: True)
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detrending_mode = Enum("linear", "quadratic")
Detrending mode (Default: “Linear”)
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lowpass_filter = Float
Lowpass filter frequency (Default: 0.01)
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highpass_filter = Float
Highpass filter frequency (Default: 0.1)
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scrubbing = Bool
Perform scrubbing (Default: True)
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class
cmp.stages.functional.functionalMRI.
FunctionalMRIStage
(bids_dir, output_dir)[source]¶ Bases:
cmp.stages.common.Stage
Class that represents the post-registration preprocessing stage of the
fMRIPipeline
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create_workflow
()[source]¶ Create the workflow of the
FunctionalMRIStage
See also
cmp.pipelines.functional.fMRI.fMRIPipeline
,cmp.stages.functional.functionalMRI.FunctionalMRIConfig
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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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