cmp.stages.preprocessing.preprocessing module

CMP preprocessing Stage (not used yet!)

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

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

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

define_inspect_outputs()[source]

Update the `inspect_outputs’ class attribute.

It contains a dictionary of stage outputs with corresponding commands for visual inspection.

has_run()[source]

Function that returns True if the stage has been run successfully.

Returns

Return type

True if the stage has been run successfully