niworkflows.interfaces.registration module

ReportCapableInterfaces for registration tools.

class niworkflows.interfaces.registration.ANTSApplyTransformsRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, niworkflows.interfaces.fixes.FixHeaderApplyTransforms

input_spec

alias of _ANTSApplyTransformsInputSpecRPT

output_spec

alias of _ANTSApplyTransformsOutputSpecRPT

class niworkflows.interfaces.registration.ANTSRegistrationRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, niworkflows.interfaces.fixes.FixHeaderRegistration

input_spec

alias of _ANTSRegistrationInputSpecRPT

output_spec

alias of _ANTSRegistrationOutputSpecRPT

class niworkflows.interfaces.registration.ApplyTOPUPRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, nipype.interfaces.fsl.epi.ApplyTOPUP

input_spec

alias of _ApplyTOPUPInputSpecRPT

output_spec

alias of _ApplyTOPUPOutputSpecRPT

class niworkflows.interfaces.registration.ApplyXFMRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.registration.FLIRTRPT, nipype.interfaces.fsl.preprocess.ApplyXFM

input_spec

alias of _ApplyXFMInputSpecRPT

output_spec

alias of _FLIRTOutputSpecRPT

class niworkflows.interfaces.registration.BBRegisterRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, nipype.interfaces.freesurfer.preprocess.BBRegister

input_spec

alias of _BBRegisterInputSpecRPT

output_spec

alias of _BBRegisterOutputSpecRPT

class niworkflows.interfaces.registration.EstimateReferenceImage(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.SimpleInterface

Generate a reference 3D map from BOLD and SBRef EPI images for BOLD datasets.

Given a 4D BOLD file or one or more 3/4D SBRefs, estimate a reference image for subsequent motion estimation and coregistration steps. For the case of BOLD datasets, it estimates a number of T1w saturated volumes (non-steady state at the beginning of the scan) and calculates the median across them. Otherwise (SBRefs or detected zero non-steady state frames), a median of of a subset of motion corrected volumes is used. If the input reference (BOLD or SBRef) is 3D already, it just returns a copy of the image with the NIfTI header extensions removed.

LIMITATION: If one wants to extract the reference from several SBRefs with several echoes each, the first echo should be selected elsewhere and run this interface in multiecho = False mode.

input_spec

alias of _EstimateReferenceImageInputSpec

output_spec

alias of _EstimateReferenceImageOutputSpec

class niworkflows.interfaces.registration.FLIRTRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, nipype.interfaces.fsl.preprocess.FLIRT

input_spec

alias of _FLIRTInputSpecRPT

output_spec

alias of _FLIRTOutputSpecRPT

class niworkflows.interfaces.registration.FUGUERPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, nipype.interfaces.fsl.preprocess.FUGUE

input_spec

alias of _FUGUEInputSpecRPT

output_spec

alias of _FUGUEOutputSpecRPT

class niworkflows.interfaces.registration.MRICoregRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, nipype.interfaces.freesurfer.registration.MRICoreg

input_spec

alias of _MRICoregInputSpecRPT

output_spec

alias of _MRICoregOutputSpecRPT

class niworkflows.interfaces.registration.ResampleBeforeAfterRPT(generate_report=True, **kwargs)[source]

Bases: niworkflows.interfaces.registration.SimpleBeforeAfterRPT

input_spec

alias of _ResampleBeforeAfterInputSpecRPT

class niworkflows.interfaces.registration.RobustMNINormalizationRPT(generate_report=False, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, niworkflows.interfaces.mni.RobustMNINormalization

input_spec

alias of _RobustMNINormalizationInputSpecRPT

output_spec

alias of _RobustMNINormalizationOutputSpecRPT

class niworkflows.interfaces.registration.SimpleBeforeAfterRPT(generate_report=True, **kwargs)[source]

Bases: niworkflows.interfaces.report_base.RegistrationRC, niworkflows.interfaces.report_base.ReportingInterface

input_spec

alias of _SimpleBeforeAfterInputSpecRPT