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”)

bandpass_filtering = Bool

Perform bandpass filtering (Default: True)

lowpass_filter = Float

Lowpass filter frequency (Default: 0.01)

highpass_filter = Float

Highpass filter frequency (Default: 0.1)

scrubbing = Bool

Perform scrubbing (Default: True)

See also

cmp.stages.functional.functionalMRI.FunctionalMRIStage

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

define_inspect_outputs()[source]

Update the inspect_outputs class attribute.

It contains a dictionary of stage outputs with corresponding commands for visual inspection.