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”])
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make_isotropic
¶ Resample to isotropic resolution (Default: False)
- Type
traits.Bool
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isotropic_vox_size
¶ Isotropic resolution to be resampled (Default: 1.2, desc=’’)
- Type
traits.Float
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isotropic_interpolation
¶ Interpolation type used for resampling that can be: ‘cubic’, ‘weighted’, ‘nearest’, ‘sinc’, or ‘interpolate’, (Default: ‘cubic’)
- Type
traits.Enum
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brain_mask_extraction_tool
¶ Choice of brain extraction tool: “Freesurfer”, “BET”, or “ANTs” (Default: Freesurfer)
- Type
traits.Enum
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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
-
brain_mask_path
¶ Custom brain mask path
- Type
traits.File
-
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_trait
¶ Freesurfer subject (being processed) directory path usually
/output_dir/freesurfer/sub-XX(_ses-YY)
- Type
traits.List
-
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
-
white_matter_mask
¶ Custom white-matter mask
- Type
traits.File
-
number_of_threads
¶ Number of threads leveraged by OpenMP and used in the stage by Freesurfer and ANTs (Default: 1)
- Type
traits.Int
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class
cmp.stages.segmentation.segmentation.
SegmentationStage
(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
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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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