Merge pull request #2784 from satra/enh/antsCT

Enh/ants ct

Author: effigies

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)

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(),

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', 

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(