cmp.stages.preprocessing.fmri_preprocessing module¶
Definition of config and stage classes for pre-registration fMRI preprocessing.
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class
cmp.stages.preprocessing.fmri_preprocessing.
PreprocessingConfig
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
PreprocessingStage
object.-
discard_n_volumes
¶ (Default: ‘5’)
- Type
traits.Int
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despiking
¶ (Default: True)
- Type
traits.Bool
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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
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repetition_time
¶ Repetition time (Default: 1.92)
- Type
traits.Float
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motion_correction
¶ Perform motion correction (Default: True)
- Type
traits.Bool
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class
cmp.stages.preprocessing.fmri_preprocessing.
PreprocessingStage
(bids_dir, output_dir)[source]¶ Bases:
cmp.stages.common.Stage
Class that represents the pre-registration preprocessing stage of a
fMRIPipeline
instance.-
create_workflow
()[source]¶ Create the workflow of the
PreprocessingStage
See also
cmp.pipelines.functional.fMRI.fMRIPipeline
,cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig
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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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