cmp.pipelines.functional.fMRI module¶
Functional pipeline Class definition.
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class
cmp.pipelines.functional.fMRI.Check_Input_Notification[source]¶ Bases:
traits.has_traits.HasTraits
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class
cmp.pipelines.functional.fMRI.Global_Configuration[source]¶ Bases:
traits.has_traits.HasTraitsGlobal pipeline configurations.
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process_type¶ Processing pipeline type
- Type
‘fMRI’
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imaging_model¶ Imaging model used by
RegistrationStage- Type
‘fMRI’
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class
cmp.pipelines.functional.fMRI.fMRIPipeline(project_info)[source]¶ Bases:
cmp.pipelines.common.PipelineClass that extends a
Pipelineand represents the processing pipeline for structural MRI.- It is composed of:
the preprocessing stage that can perform slice timing correction, deskiping and motion correction
the registration stage that co-registered the anatomical T1w scan to the mean BOLD image and projects the parcellations to the native fMRI space
the extra-preprocessing stage (FunctionalMRIStage) that can perform nuisance regression and bandpass filtering
the connectome stage that extracts the time-series of each parcellation ROI and computes the Pearson’s correlation coefficient between ROI time-series to create the functional connectome.
See also
cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage,cmp.stages.registration.registration.RegistrationStage,cmp.stages.functional.functionalMRI.FunctionalMRIStage,cmp.stages.connectome.fmri_connectome.ConnectomeStage-
check_input(layout, gui=True, debug=False)[source]¶ Check if input of the diffusion pipeline are available.
- Parameters
layout (bids.BIDSLayout) – Instance of BIDSLayout
gui (traits.Bool) – Boolean used to display different messages but not really meaningful anymore since the GUI components have been migrated to
cmp.bidsappmanager
- Returns
valid_inputs – True if inputs are available
- Return type
traits.Bool
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create_pipeline_flow(cmp_deriv_subject_directory, nipype_deriv_subject_directory)[source]¶ Create the pipeline workflow.
- Parameters
<Directory> (nipype_deriv_subject_directory) – Main CMP output directory of a subject e.g.
/output_dir/cmp/sub-XX/(ses-YY)<Directory> – Intermediate Nipype output directory of a subject e.g.
/output_dir/nipype/sub-XX/(ses-YY)
- Returns
An instance of
nipype.pipeline.engine.Workflow- Return type
fMRI_flow <nipype.pipeline.engine.Workflow>
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define_custom_mapping(custom_last_stage)[source]¶ Define the pipeline to be executed until a specific stages.
Not used yet by CMP3.
- Parameters
custom_last_stage (string) – Last stage to execute. Valid values are: “Preprocessing”, “Registration”, “FunctionalMRI” and “Connectome”.
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global_conf= <cmp.pipelines.functional.fMRI.Global_Configuration object>¶
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input_folders= ['anat', 'func']¶
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now= '20210308_0637'¶
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ordered_stage_list= ['Preprocessing', 'Registration', 'FunctionalMRI', 'Connectome']¶