cmp.stages.preprocessing.preprocessing module
Definition of config and stage classes for diffusion MRI preprocessing.
- 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
- description
Description (Default: ‘description’)
- Type
traits.Str
- denoising
Perform diffusion MRI denoising (Default: False)
- Type
traits.Bool
- denoising_algo
Type of denoising algorithm (Default: ‘MRtrix (MP-PCA)’)
- Type
traits.Enum([‘MRtrix (MP-PCA)’, ‘Dipy (NLM)’])
- dipy_noise_model
Type of noise model when Dipy denoising is performed that can be: ‘Rician’ or ‘Gaussian’ (Default: ‘Rician’)
- Type
traits.Enum
- bias_field_correction
Perform diffusion MRI bias field correction (Default: False)
- Type
traits.Bool
- 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’])
- eddy_current_and_motion_correction
Perform eddy current and motion correction (Default: True)
- Type
traits.Bool
- 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
- eddy_correct_motion_correction
Perform eddy current and motion correction MIGHT BE OBSOLETE (Default: True)
- Type
traits.Bool
- partial_volume_estimation
Estimate partial volume maps from brain tissues segmentation (Default: True)
- Type
traits.Bool
- fast_use_priors
Use priors when FAST is used for partial volume estimation (Default: True)
- Type
traits.Bool
- resampling
Tuple describing the target resolution (Default: (1, 1, 1))
- Type
traits.Tuple
- interpolation
Type of interpolation used when resampling that can be: ‘interpolate’, ‘weighted’, ‘nearest’, ‘sinc’, or ‘cubic’ (Default: ‘interpolate’)
- Type
traits.Enum
- tracking_tool
Tool used for tractography
- Type
Enum([‘Dipy’, ‘MRtrix’])
- act_tracking
True if Anatomically-Constrained or Particle Filtering Tractography is enabled (Default: False)
- Type
Bool
- gmwmi_seeding
True if tractography seeding is performed from the gray-matter / white-matter interface (Default: False)
- Type
Bool
- 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
- 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