in fact masking wasn't working, HistogramRegistration takes mask as numpy not nibabel

Author: bpinsard

nipype/interfaces/nipy/utils.py

@@ -73,24 +73,20 @@ def _run_interface(self, runtime):
         vol2_nii = nb.load(self.inputs.volume2)
 
         if isdefined(self.inputs.mask1):
-            mask1_nii = nb.load(self.inputs.mask1)
-            mask1_nii = nb.Nifti1Image(nb.load(self.inputs.mask1).get_data() == 1, mask1_nii.get_affine(),
-                                       mask1_nii.get_header())
+            mask1 = nb.load(self.inputs.mask1).get_data() == 1
         else:
-            mask1_nii = None
+            mask1 = None
 
         if isdefined(self.inputs.mask2):
-            mask2_nii = nb.load(self.inputs.mask2)
-            mask2_nii = nb.Nifti1Image(nb.load(self.inputs.mask2).get_data() == 1, mask2_nii.get_affine(),
-                                       mask2_nii.get_header())
+            mask2 = nb.load(self.inputs.mask2).get_data() == 1
         else:
-            mask2_nii = None
+            mask2 = None
 
         histreg = HistogramRegistration(from_img = vol1_nii,
                                         to_img = vol2_nii,
                                         similarity=self.inputs.metric,
-                                        from_mask = mask1_nii,
-                                        to_mask = mask2_nii)
+                                        from_mask = mask1,
+                                        to_mask = mask2)
         self._similarity = histreg.eval(Affine())
 
         return runtime