enh: add extracted brain to antsCorticalThickness

Author: satra

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(),