FIX: Allows for aseg to be copied in segstats for 5.3.

Author: David Ellis

nipype/interfaces/freesurfer/model.py

@@ -796,6 +796,8 @@ class SegStatsReconAllInputSpec(SegStatsInputSpec):
                    desc="Input file must be <subject_id>/surf/lh.pial")
     rh_pial = File(mandatory=True, exists=True,
                    desc="Input file must be <subject_id>/surf/rh.pial")
+    aseg = File(exists=True,
+                desc="Mandatory implicit input in 5.3")
     copy_inputs = traits.Bool(desc="If running as a node, set this to True " +
                               "otherwise, this will copy the implicit inputs " +
                               "to the node directory.")
@@ -868,6 +870,8 @@ def run(self, **inputs):
                          'mri', 'ribbon.mgz')
             copy2subjdir(self, self.inputs.presurf_seg,
                          'mri', 'aseg.presurf.mgz')
+            copy2subjdir(self, self.inputs.aseg,
+                         'mri', 'aseg.mgz')
             copy2subjdir(self, self.inputs.transform,
                          os.path.join('mri', 'transforms'),
                          'talairach.xfm')

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -638,7 +638,6 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
     ar3_wf.connect([(apas_2_aseg, segstats, [('out_file', 'segmentation_file')]),
                     (inputspec, segstats, [('lh_white', 'lh_white'),
                                            ('rh_white', 'rh_white'),
-                                           ('aseg_presurf', 'presurf_seg'),
                                            ('transform', 'transform'),
                                            ('norm', 'in_intensity'),
                                            ('norm', 'partial_volume_file'),
@@ -654,6 +653,12 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                                            ]),
                     ])
 
+    if fsvernum > 6:
+        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'presurf_seg')
+    else:
+        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'aseg')
+
+
     # White Matter Parcellation
 
     # Adds WM Parcellation info into the aseg and computes stat.