cmp.stages.segmentation.segmentation module
Definition of config and stage classes for segmentation.
- class cmp.stages.segmentation.segmentation.SegmentationConfig[source]
Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
SegmentationStage
object.- seg_tool
Choice of segmentation tool that can be “Freesurfer”
- Type
traits.Enum([“Freesurfer”, “Custom segmentation”])
- make_isotropic
Resample to isotropic resolution (Default: False)
- Type
traits.Bool
- isotropic_vox_size
Isotropic resolution to be resampled (Default: 1.2, desc=’’)
- Type
traits.Float
- isotropic_interpolation
Interpolation type used for resampling that can be: ‘cubic’, ‘weighted’, ‘nearest’, ‘sinc’, or ‘interpolate’, (Default: ‘cubic’)
- Type
traits.Enum
- brain_mask_extraction_tool
Choice of brain extraction tool: “Freesurfer”, “BET”, or “ANTs” (Default: Freesurfer)
- Type
traits.Enum
- ants_templatefile
Anatomical template used by ANTS brain extraction
- Type
traits.File
- ants_probmaskfile
Brain probability mask used by ANTS brain extraction
- Type
traits.File
- ants_regmaskfile
Mask (defined in the template space) used during registration in ANTs brain extraction. To limit the metric computation to a specific region.
- Type
traits.File
- use_fsl_brain_mask
Use FSL BET for brain extraction (Default: False)
- Type
traits.Bool
- use_existing_freesurfer_data
(Default: False)
- Type
traits.Bool
- freesurfer_subjects_dir
Freesurfer subjects directory path usually
/output_dir/freesurfer
- Type
traits.Str
- freesurfer_subject_id
Freesurfer subject (being processed) ID in the form
sub-XX(_ses-YY)
- Type
traits.Str
- freesurfer_args
Extra Freesurfer
recon-all
arguments- Type
traits.Str
- custom_brainmask
Instance of
CustomBrainMaskBIDSFile
that describes the custom BIDS formatted brain mask- Type
traits.Instance(CustomBrainMaskBIDSFile)
- custom_wm_mask
Instance of
CustomWMMaskBIDSFile
that describes the custom BIDS formatted white-matter mask- Type
traits.Instance(CustomWMMaskBIDSFile)
- custom_gm_mask
Instance of
CustomGMMaskBIDSFile
that describes the custom BIDS formatted gray-matter mask- Type
traits.Instance(CustomGMMaskBIDSFile)
- custom_csf_mask
Instance of
CustomCSFMaskBIDSFile
that describes the custom BIDS formatted CSF mask- Type
traits.Instance(CustomCSFMaskBIDSFile)
- custom_aparcaseg
Instance of
CustomAparcAsegBIDSFile
that describes the custom BIDS formatted Freesurfer aparc-aseg file- Type
traits.Instance(CustomAparcAsegBIDSFile)
- number_of_threads
Number of threads leveraged by OpenMP and used in the stage by Freesurfer and ANTs (Default: 1)
- Type
traits.Int
- class cmp.stages.segmentation.segmentation.SegmentationStage(subject, session, bids_dir, output_dir)[source]
Bases:
cmp.stages.common.Stage
Class that represents the segmentation stage of a
AnatomicalPipeline
.- create_workflow()[source]
Create the workflow of the
SegmentationStage
See also
cmp.pipelines.anatomical.anatomical.AnatomicalPipeline
,cmp.stages.segmentation.segmentation.SegmentationConfig
- 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 segmentation stage
outputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the outputs of the segmentation stage
- create_workflow_custom(flow, inputnode, 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
inputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the inputs of the segmentation stage
outputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the outputs of the segmentation stage