cmp.stages.preprocessing.fmri_preprocessing module

Definition of config and stage classes for pre-registration fMRI preprocessing.

class cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig

Bases: traits.has_traits.HasTraits

Class used to store configuration parameters of a PreprocessingStage object.

discard_n_volumes

(Default: ‘5’)

Type

traits.Int

despiking

(Default: True)

Type

traits.Bool

slice_timing

Slice acquisition order for slice timing correction that can be: “bottom-top interleaved”, “bottom-top interleaved”, “top-bottom interleaved”, “bottom-top”, and “top-bottom” (Default: “none”)

Type

traits.Enum

repetition_time

Repetition time (Default: 1.92)

Type

traits.Float

motion_correction

Perform motion correction (Default: True)

Type

traits.Bool

See also

cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage

class cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage(bids_dir, output_dir)

Bases: cmp.stages.common.Stage

Class that represents the pre-registration preprocessing stage of a fMRIPipeline instance.

create_workflow()

Create the workflow of the PreprocessingStage

See also

cmp.pipelines.functional.fMRI.fMRIPipeline, cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig

create_workflow(flow, inputnode, outputnode)

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()

Update the `inspect_outputs’ class attribute.

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

has_run()

Function that returns True if the stage has been run successfully.

Returns

Return type

True if the stage has been run successfully