cmp.stages.parcellation.parcellation module
Definition of config and stage classes for computing brain parcellation.
- 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”])
- parcellation_scheme
Parcellation scheme used (Default: ‘Lausanne2018’)
- Type
traits.Str
- parcellation_scheme_editor
Choice of parcellation schemes
- Type
traits.List([‘NativeFreesurfer’, ‘Lausanne2018’, ‘Custom’])
- include_thalamic_nuclei_parcellation
Perform and include thalamic nuclei segmentation in ‘Lausanne2018’ parcellation (Default: True)
- Type
traits.Bool
- 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’])
- segment_hippocampal_subfields
Perform and include FreeSurfer hippocampal subfields segmentation in ‘Lausanne2018’ parcellation (Default: True)
- Type
traits.Bool
- segment_brainstem
Perform and include FreeSurfer brainstem segmentation in ‘Lausanne2018’ parcellation (Default: True)
- Type
traits.Bool
- atlas_info
Dictionary storing information of atlases in the form >>> atlas_info = { >>> “atlas_name”: { >>> ‘number_of_regions’: 83, >>> ‘node_information_graphml’: “/path/to/file.graphml” >>> } >>> } # doctest: +SKIP
- Type
traits.Dict
- custom_parcellation
Instance of
CustomParcellationBIDSFile
that describes the custom BIDS-formatted brain parcellation file- Type
traits.Instance(CustomParcellationBIDSFile)
- class cmp.stages.parcellation.parcellation.ParcellationStage(pipeline_mode, subject, session, 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
- create_workflow(flow, inputnode, outputnode)[source]
Create the stage workflow.
- 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 parcellation stage
outputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the outputs of the parcellation stage
- create_workflow_custom(flow, outputnode)[source]
Create the stage workflow when custom inputs are specified.
- Parameters
flow (nipype.pipeline.engine.Workflow) – The nipype.pipeline.engine.Workflow instance of the anatomical pipeline
outputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the outputs of the parcellation stage