cmp.stages.parcellation.parcellation module¶
Definition of config and stage classes for computing brain parcellation.
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class
cmp.stages.parcellation.parcellation.
ParcellationConfig
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
ParcellationStage
object.-
pipeline_mode
¶ Distinguish if a parcellation is run in a “Diffusion” or in a fMRI pipeline
- Type
traits.Enum([“Diffusion”, “fMRI”])
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parcellation_scheme
¶ Parcellation scheme used (Default: ‘Lausanne2008’)
- Type
traits.Str
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parcellation_scheme_editor
¶ Choice of parcellation schemes
- Type
traits.List([‘NativeFreesurfer’, ‘Lausanne2008’, ‘Lausanne2018’])
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include_thalamic_nuclei_parcellation
¶ Perform and include thalamic nuclei segmentation in ‘Lausanne2018’ parcellation (Default: True)
- Type
traits.Bool
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ants_precision_type
¶ Specify ANTs used by thalamic nuclei segmentation to adopt single / double precision float representation to reduce memory usage. (Default: ‘double’)
- Type
traits.Enum([‘double’, ‘float’])
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segment_hippocampal_subfields
¶ Perform and include FreeSurfer hippocampal subfields segmentation in ‘Lausanne2018’ parcellation (Default: True)
- Type
traits.Bool
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segment_brainstem
¶ Perform and include FreeSurfer brainstem segmentation in ‘Lausanne2018’ parcellation (Default: True)
- Type
traits.Bool
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atlas_info
¶ Dictionary storing information of atlases in the form >>> atlas_info = {atlas_name: {‘number_of_regions’: number_of_regions, >>> ‘node_information_graphml’: graphml_file}} # doctest: +SKIP
- Type
traits.Dict
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update_atlas_info
()[source]¶ Update
atlas_info
class attribute.
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class
cmp.stages.parcellation.parcellation.
ParcellationStage
(pipeline_mode, bids_dir, output_dir)[source]¶ Bases:
cmp.stages.common.Stage
Class that represents the parcellation stage of a
AnatomicalPipeline
.-
create_workflow
()[source]¶ Create the workflow of the
ParcellationStage
See also
cmp.pipelines.anatomical.anatomical.AnatomicalPipeline
,cmp.stages.parcellation.parcellation.ParcellationConfig
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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 anatomical 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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