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)