cmp.stages.registration.registration module¶
Definition of config and stage classes for MRI co-registration
-
class
cmp.stages.registration.registration.
RegistrationConfig
[source]¶ Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
RegistrationStage
instance.-
pipeline
¶ Pipeline type (Default: “Diffusion”)
- Type
traits.Enum([“Diffusion”, “fMRI”])
-
registration_mode_trait
¶ Choices of registration tools updated depending on the
pipeline
type. (Default: [‘FSL’, ‘ANTs’] if “Diffusion”, [‘FSL’, ‘BBregister (FS)’] if “fMRI”)- Type
traits.List([‘FSL’, ‘ANTs’, ‘BBregister (FS)’])
-
registration_mode
¶ Registration tool used from the
registration_mode_trait
list (Default: ‘ANTs’)- Type
traits.Str
-
diffusion_imaging_model
¶ Diffusion imaging model (‘DTI’ for instance)
- Type
traits.Str
-
use_float_precision
¶ Use ‘single’ instead of ‘double’ float representation to reduce memory usage of ANTs (Default: False)
- Type
traits.Bool
-
ants_interpolation
¶ Interpolation type used by ANTs that can be: ‘Linear’, ‘NearestNeighbor’, ‘CosineWindowedSinc’, ‘WelchWindowedSinc’, ‘HammingWindowedSinc’, ‘LanczosWindowedSinc’, ‘BSpline’, ‘MultiLabel’, or ‘Gaussian’ (Default: ‘Linear’)
- Type
traits.Enum
-
ants_bspline_interpolation_parameters
¶ ANTs BSpline interpolation parameters (Default: traits.Tuple(Int(3)))
- Type
traits.Tuple
-
ants_gauss_interpolation_parameters
¶ ANTs Gaussian interpolation parameters (Default: traits.Tuple(Float(5), Float(5)))
- Type
traits.Tuple
-
ants_multilab_interpolation_parameters
¶ ANTs Multi-label interpolation parameters (Default: traits.Tuple(Float(5), Float(5)))
- Type
traits.Tuple
-
ants_lower_quantile
¶ ANTs lower quantile (Default: 0.005)
- Type
traits.Float
-
ants_upper_quantile
¶ ANTs upper quantile (Default: 0.995)
- Type
traits.Float
-
ants_convergence_thresh
¶ ANTs convergence threshold (Default: 1e-06)
- Type
traits.Float
-
ants_convergence_winsize
¶ ANTs convergence window size (Default: 10)
- Type
traits.Int
-
ants_linear_gradient_step
¶ ANTS linear gradient step size (Default: 0.1)
- Type
traits.Float
-
ants_linear_cost
¶ Metric used by ANTs linear registration phase that can be ‘CC’, ‘MeanSquares’, ‘Demons’, ‘GC’, ‘MI’, or ‘Mattes’ (Default: ‘MI’)
- Type
traits.Enum
-
ants_linear_sampling_strategy
¶ ANTS sampling strategy for the linear registration phase that can be ‘None’, ‘Regular’, or ‘Random’ (Default: ‘Regular’)
- Type
traits.Enum
-
ants_linear_sampling_perc
¶ Percentage used if random sampling strategy is employed in the linear registration phase (Default: 0.25)
- Type
traits.Float
-
ants_perform_syn
¶ (Default: True)
- Type
traits.Bool
-
ants_nonlinear_gradient_step
¶ (Default: 0.1)
- Type
traits.Float
-
ants_nonlinear_cost
¶ Metric used by ANTs nonlinear (SyN) registration phase that can be ‘CC’, ‘MeanSquares’, ‘Demons’, ‘GC’, ‘MI’, or ‘Mattes’ (Default: ‘CC’)
- Type
traits.Enum
-
ants_nonlinear_update_field_variance
¶ Weight to update field variance in ANTs nonlinear (SyN) registration phase (Default: 3.0)
- Type
traits.Float
-
ants_nonlinear_total_field_variance
¶ Weight to give to total field variance in ANTs nonlinear (SyN) registration phase (Default: 0.0)
- Type
traits.Float
-
flirt_args
¶ FLIRT extra arguments that will be append to the FSL FLIRT command (Default: None)
- Type
traits.Str
-
uses_qform
¶ FSL FLIRT uses qform (Default: True)
- Type
traits.Bool
-
dof
¶ Specify number of degree-of-freedom to FSL FLIRT (Default: 6)
- Type
traits.Int
-
fsl_cost
¶ Metric used by FSL registration that can be ‘mutualinfo’, ‘corratio’, ‘normcorr’, ‘normmi’, ‘leastsq’, or ‘labeldiff’ (Default: ‘normmi’)
- Type
traits.Enum
-
no_search
¶ Enable FSL FLIRT “no search” option (Default: True)
- Type
traits.Bool
-
init
¶ Initialization type of FSL registration: ‘spm’, ‘fsl’, or ‘header’ (Default: ‘smp’)
- Type
traits.Enum(‘header’, [‘spm’, ‘fsl’, ‘header’])
-
contrast_type
¶ Contrast type specified to BBRegister: ‘t1’, ‘t2’, or ‘dti’ (Default: ‘dti’)
- Type
traits.Enum(‘dti’, [‘t1’, ‘t2’, ‘dti’])
-
apply_to_eroded_wm
¶ Apply estimated transform to eroded white-matter mask (Default: True)
- Type
traits.Bool
-
apply_to_eroded_csf
¶ Apply estimated transform to eroded cortico spinal fluid mask (Default: True)
- Type
traits.Bool
-
apply_to_eroded_brain
¶ Apply estimated transform to eroded brain mask (Default: False)
- Type
traits.Bool
-
-
class
cmp.stages.registration.registration.
RegistrationStage
(pipeline_mode, fs_subjects_dir=None, fs_subject_id=None, bids_dir='', output_dir='')[source]¶ Bases:
cmp.stages.common.Stage
Class that represents the registration stage of both
DiffusionPipeline
andfMRIPipeline
.-
fs_subjects_dir
¶ Freesurfer subjects directory (needed by BBRegister)
- Type
traits.Directory
-
fs_subject_id
¶ Freesurfer subject (being processed) directory (needed by BBRegister)
- Type
traits.Str
-
create_workflow
()[source]¶ Create the workflow of the
RegistrationStage
See also
cmp.pipelines.diffusion.diffusion.DiffusionPipeline
,cmp.pipelines.functional.fMRI.fMRIPipeline
,cmp.stages.registration.registration.RegistrationConfig
-
create_workflow
(flow, inputnode, outputnode)[source]¶ Create the stage worflow.
- Parameters
flow (nipype.pipeline.engine.Workflow) – The nipype.pipeline.engine.Workflow instance of either the Diffusion pipeline or the fMRI 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
-