FIX: Removes in_aseg from ribbon masking.

Author: ellisdg

nipype/interfaces/freesurfer/utils.py

@@ -2363,7 +2363,8 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.rh_pial, 'surf', 'rh.pial')
             copy2subjdir(self, self.inputs.lh_white, 'surf', 'lh.white')
             copy2subjdir(self, self.inputs.rh_white, 'surf', 'rh.white')
-            copy2subjdir(self, self.inputs.in_aseg, 'mri')
+            if isdefined(self.inputs.in_aseg):
+                copy2subjdir(self, self.inputs.in_aseg, 'mri')
         return super(VolumeMask, self).run(**inputs)
 
     def _format_arg(self, name, spec, value):

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -8,7 +8,7 @@
 from nipype.interfaces.io import DataGrabber
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
-                      th3=True, exvivo=True, entorhinal=True):
+                      th3=True, exvivo=True, entorhinal=True, fsvernum=5.3):
 
     # AutoRecon3
     # Workflow
@@ -274,14 +274,15 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
     volume_mask.inputs.copy_inputs = True
 
 
-    ar3_wf.connect([(inputspec, volume_mask, [('aseg_presurf', 'in_aseg'),
-                                              ('lh_white', 'lh_white'),
-                                              ('rh_white', 'rh_white'),
-                                               ]),
+    ar3_wf.connect([(inputspec, volume_mask, [('lh_white', 'lh_white'),
+                                              ('rh_white', 'rh_white')]),
                     (ar3_lh_wf1, volume_mask, [('outputspec.pial', 'lh_pial')]),
                     (ar3_rh_wf1, volume_mask, [('outputspec.pial', 'rh_pial')]),
                     ])
 
+    if fsvernum > 6:
+        ar3_wf.connect([(inputpsec, volume_mask, [('aseg_presurf', 'in_aseg')])])
+
     ar3_lh_wf2 = pe.Workflow(name="AutoRecon3_Left_2")
     ar3_rh_wf2 = pe.Workflow(name="AutoRecon3_Right_2")
 

nipype/workflows/smri/freesurfer/recon.py

@@ -274,7 +274,8 @@ def checkarg(arg, default):
 
     # create AutoRecon3
     ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=th3,
-                                            exvivo=exvivo, entorhinal=entorhinal)
+                                            exvivo=exvivo, entorhinal=entorhinal,
+                                            fsvernum=fsvernum)
     # connect inputs for AutoRecon3
     reconall.connect([(config_node, ar3_wf, [('lh_atlas', 'inputspec.lh_atlas'),
                                              ('rh_atlas', 'inputspec.rh_atlas'),