@@ -113,9 +113,9 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
 'rhe "Optimized Shooting - superlarge ventricles" option for "Spatial registration" is ! '
 "required Values: \nnone: 0;\nlight: 1;\nfull: 2;\ndefault: 1070."
 )
-initial_segmentation = traits.Int(
-0, field="extopts.spm_kamap", desc=_help_initial_seg, usedefault=True
-)
+# initial_segmentation = traits.Int(
+# 0, field="extopts.spm_kamap", desc=_help_initial_seg, usedefault=True
+# )
 
 _help_las = (
 "Additionally to WM-inhomogeneities, GM intensity can vary across different regions such as the motor"
@@ -232,10 +232,8 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
 surface_measures = traits.Int(
 1,
 field="output.surf_measures",
-# usedefault=True,
+usedefault=True,
 desc="Extract surface measures",
-# requires=["neuromorphometrics", "lpba40", "cobra", "hammers", "thalamus", "thalamic_nuclei", "suit", "ibsr"],
-# xor=["noROI"],
 )
 
 # Templates
@@ -244,64 +242,64 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
 field="output.ROImenu.atlases.neuromorphometrics",
 # usedefault=True,
 desc="Extract brain measures for Neuromorphometrics template",
-xor=["noROI"],
+xor=["noROI"]
 )
 lpba40 = traits.Bool(
 True,
 field="output.ROImenu.atlases.lpba40",
 # usedefault=True,
 desc="Extract brain measures for LPBA40 template",
-xor=["noROI"],
+xor=["noROI"]
 )
 cobra = traits.Bool(
 True,
 field="output.ROImenu.atlases.hammers",
 # usedefault=True,
 desc="Extract brain measures for COBRA template",
-xor=["noROI"],
+xor=["noROI"]
 )
 hammers = traits.Bool(
 False,
 field="output.ROImenu.atlases.cobra",
 # usedefault=True,
 desc="Extract brain measures for Hammers template",
-xor=["noROI"],
+xor=["noROI"]
 )
 thalamus = traits.Bool(
 True,
 field="output.ROImenu.atlases.thalamus",
 # usedefault=True,
 desc="Extract brain measures for Thalamus template",
-xor=["noROI"],
+xor=["noROI"]
 )
 thalamic_nuclei = traits.Bool(
 True,
-field="output.ROImenu.atlases.thalamaic_nuclei",
+field="output.ROImenu.atlases.thalamic_nuclei",
 # usedefault=True,
 desc="Extract brain measures for Thalamic Nuclei template",
-xor=["noROI"],
+xor=["noROI"]
 )
 suit = traits.Bool(
 True,
 field="output.ROImenu.atlases.suit",
 # usedefault=True,
 desc="Extract brain measures for Suit template",
-xor=["noROI"],
+xor=["noROI"]
 )
 ibsr = traits.Bool(
 False,
 field="output.ROImenu.atlases.ibsr",
 # usedefault=True,
 desc="Extract brain measures for IBSR template",
-xor=["noROI"],
+xor=["noROI"]
 )
 own_atlas = InputMultiPath(
 ImageFileSPM(exists=True),
 field="output.ROImenu.atlases.ownatlas",
 desc="Extract brain measures for a given template",
 mandatory=False,
 copyfile=False,
-xor=["noROI"],
+xor=["noROI"]
 )
 noROI = traits.Bool(
 field="output.ROImenu.noROI",
@@ -574,9 +572,10 @@ def _format_arg(self, opt, spec, val):
 def _list_outputs(self):
 outputs = self._outputs().get()
 f = self.inputs.in_files[0]
-pth, base, ext = split_filename(f)
 if '.nii.gz' in f:
 f = f[:-3]
+pth, base, ext = split_filename(f)
+
 outputs["mri_images"] = [
 str(mri) for mri in Path(pth).glob("mri/*") if mri.is_file()
 ]
@@ -626,14 +625,17 @@ def _list_outputs(self):
 outputs["label_files"] = [
 str(label) for label in Path(pth).glob("label/*") if label.is_file()
 ]
+
+if self.inputs.neuromorphometrics or self.inputs.lpba40 or self.inputs.cobra or self.inputs.hammers or self.inputs.thalamus or self.inputs.thalamic_nuclei or self.inputs.suit or self.inputs.ibsr:
+outputs["label_roi"] = fname_presuffix(
+f, prefix=os.path.join("label", "catROI_"), suffix=".xml", use_ext=False
+)
 
-if self.inputs.noROI:
+if self.inputs.surface_and_thickness_estimation:
 outputs["label_rois"] = fname_presuffix(
 f, prefix=os.path.join("label", "catROIs_"), suffix=".xml", use_ext=False
 )
-outputs["label_roi"] = fname_presuffix(
-f, prefix=os.path.join("label", "catROI_"), suffix=".xml", use_ext=False
-)
+
 
 return outputs