cmp.stages.functional.functionalMRI module
Definition of config and stage classes for the extra functional preprocessing stage.
- 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
- csf
Perform CSF nuisance regression (Default: True)
- Type
traits.Bool
- wm
Perform White-Matter nuisance regression (Default: True)
- Type
traits.Bool
- motion
Perform motion nuisance regression (Default: True)
- Type
traits.Bool
- detrending = Bool
Perform detrending (Default: True)
- detrending_mode = Enum("linear", "quadratic")
Detrending mode (Default: “Linear”)
- lowpass_filter = Float
Lowpass filter frequency (Default: 0.01)
- highpass_filter = Float
Highpass filter frequency (Default: 0.1)
- scrubbing = Bool
Perform scrubbing (Default: True)
- 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
.- create_workflow()[source]
Create the workflow of the
FunctionalMRIStage
See also
cmp.pipelines.functional.fMRI.fMRIPipeline
,cmp.stages.functional.functionalMRI.FunctionalMRIConfig
- 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