diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py index 04d212ec0f..743f0a3903 100644 --- a/nipype/interfaces/ants/segmentation.py +++ b/nipype/interfaces/ants/segmentation.py @@ -560,6 +560,7 @@ class CorticalThicknessInputSpec(ANTSCommandInputSpec): class CorticalThicknessOutputSpec(TraitedSpec): BrainExtractionMask = File(exists=True, desc='brain extraction mask') + ExtractedBrainN4 = File(exists=True, desc='extracted brain from N4 image') BrainSegmentation = File(exists=True, desc='brain segmentaion image') BrainSegmentationN4 = File(exists=True, desc='N4 corrected image') BrainSegmentationPosteriors = OutputMultiPath( @@ -645,6 +646,9 @@ def _list_outputs(self): outputs['BrainExtractionMask'] = os.path.join( os.getcwd(), self.inputs.out_prefix + 'BrainExtractionMask.' + self.inputs.image_suffix) + outputs['ExtractedBrainN4'] = os.path.join( + os.getcwd(), self.inputs.out_prefix + 'ExtractedBrain0N4.' + + self.inputs.image_suffix) outputs['BrainSegmentation'] = os.path.join( os.getcwd(), self.inputs.out_prefix + 'BrainSegmentation.' + self.inputs.image_suffix) diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index dd39568bc0..e2595a710f 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -75,6 +75,7 @@ def test_CorticalThickness_outputs(): BrainVolumes=dict(), CorticalThickness=dict(), CorticalThicknessNormedToTemplate=dict(), + ExtractedBrainN4=dict(), SubjectToTemplate0GenericAffine=dict(), SubjectToTemplate1Warp=dict(), SubjectToTemplateLogJacobian=dict(), diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py index 5330c67e34..d23887c890 100644 --- a/nipype/interfaces/spm/preprocess.py +++ b/nipype/interfaces/spm/preprocess.py @@ -524,12 +524,12 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec): est_re_est_mov_par = traits.Bool( field='uweoptions.rem', desc='Re-estimate movement parameters at each unwarping iteration.') - est_num_of_interations = traits.ListInt( + est_num_of_iterations = traits.ListInt( [5], field='uweoptions.noi', minlen=1, maxlen=1, - usedfault=True, + usedefault=True, desc='Number of iterations.') est_taylor_expansion_point = traits.String( 'Average', diff --git a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py index 50b56b81e1..5c7c36f80b 100644 --- a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py +++ b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py @@ -8,11 +8,11 @@ def test_RealignUnwarp_inputs(): est_basis_func=dict(field='uweoptions.basfcn', ), est_first_order_effects=dict(field='uweoptions.fot', ), est_jacobian_deformations=dict(field='uweoptions.jm', ), - est_num_of_interations=dict( + est_num_of_iterations=dict( field='uweoptions.noi', maxlen=1, minlen=1, - usedfault=True, + usedefault=True, ), est_re_est_mov_par=dict(field='uweoptions.rem', ), est_reg_factor=dict(