cmp.stages.preprocessing.preprocessing module¶
CMP preprocessing Stage (not used yet!)
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class
cmp.stages.preprocessing.preprocessing.
PreprocessingConfig
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
PreprocessingStage
instance.-
total_readout
¶ Acquisition total readout time used by FSL Eddy (Default: 0.0)
- Type
traits.Float
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description
¶ Description (Default: ‘description’)
- Type
traits.Str
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denoising
¶ Perform diffusion MRI denoising (Default: False)
- Type
traits.Bool
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denoising_algo
¶ Type of denoising algorithm (Default: ‘MRtrix (MP-PCA)’)
- Type
traits.Enum([‘MRtrix (MP-PCA)’, ‘Dipy (NLM)’])
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dipy_noise_model
¶ Type of noise model when Dipy denoising is performed that can be: ‘Rician’ or ‘Gaussian’ (Default: ‘Rician’)
- Type
traits.Enum
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bias_field_correction
¶ Perform diffusion MRI bias field correction (Default: False)
- Type
traits.Bool
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bias_field_algo
¶ Type of bias field correction algorithm that can be: ‘ANTS N4’ or ‘FSL FAST’ (Default: ‘ANTS N4’)
- Type
traits.Enum, [‘ANTS N4’, ‘FSL FAST’])
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eddy_current_and_motion_correction
¶ Perform eddy current and motion correction (Default: True)
- Type
traits.Bool
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eddy_correction_algo
¶ Algorithm used for eddy current correction that can be: ‘FSL eddy_correct’ or ‘FSL eddy’ (Default: ‘FSL eddy_correct’)
- Type
traits.Enum
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eddy_correct_motion_correction
¶ Perform eddy current and motion correction MIGHT BE OBSOLETE (Default: True)
- Type
traits.Bool
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partial_volume_estimation
¶ Estimate partial volume maps from brain tissues segmentation (Default: True)
- Type
traits.Bool
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fast_use_priors
¶ Use priors when FAST is used for partial volume estimation (Default: True)
- Type
traits.Bool
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resampling
¶ Tuple describing the target resolution (Default: (1, 1, 1))
- Type
traits.Tuple
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interpolation
¶ Type of interpolation used when resampling that can be: ‘interpolate’, ‘weighted’, ‘nearest’, ‘sinc’, or ‘cubic’ (Default: ‘interpolate’)
- Type
traits.Enum
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class
cmp.stages.preprocessing.preprocessing.
PreprocessingStage
(bids_dir, output_dir)[source]¶ Bases:
cmp.stages.common.Stage
Class that represents the pre-registration preprocessing stage of a
DiffusionPipeline
instance.-
create_workflow
()[source]¶ Create the workflow of the
PreprocessingStage
See also
cmp.pipelines.diffusion.diffusion.DiffusionPipeline
,cmp.stages.preprocessing.preprocessing.PreprocessingConfig
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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 Diffusion 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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