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: ‘Lausanne2008’)

Type

traits.Str

parcellation_scheme_editor

Choice of parcellation schemes

Type

traits.List([‘NativeFreesurfer’, ‘Lausanne2008’, ‘Lausanne2018’])

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’: number_of_regions, >>> ‘node_information_graphml’: graphml_file}} # doctest: +SKIP

Type

traits.Dict

update_atlas_info()[source]

Update atlas_info class attribute.

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

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

define_inspect_outputs()[source]

Update the `inspect_outputs’ class attribute.

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

has_run()[source]

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

Returns

Return type

True if the stage has been run successfully