FIX: Adds filled input to Aparc2Aseg.

Author: David Ellis

nipype/interfaces/freesurfer/utils.py

@@ -2742,6 +2742,8 @@ class Aparc2AsegInputSpec(FSTraitedSpec):
     rh_annotation = File(mandatory=True, exists=True,
                          desc="Input file must be <subject_id>/label/rh.aparc.annot")
     # optional
+    filled = File(exists=True,
+                  desc="Implicit input filled file. Only required with FS v5.3.")
     aseg = File(argstr="--aseg %s", mandatory=False, exists=True,
                 desc="Input aseg file")
     volmask = traits.Bool(argstr="--volmask", mandatory=False,
@@ -2824,6 +2826,7 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.rh_ribbon, 'mri', 'rh.ribbon.mgz')
             copy2subjdir(self, self.inputs.ribbon, 'mri', 'ribbon.mgz')
             copy2subjdir(self, self.inputs.aseg, 'mri')
+            copy2subjdir(self, self.inputs.filled, 'mri', 'filled.mgz')
             copy2subjdir(self, self.inputs.lh_annotation, 'label')
             copy2subjdir(self, self.inputs.rh_annotation, 'label')
 

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -685,6 +685,9 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     (aparc_2_aseg, wm_parcellation, [('out_file', 'ctxseg')])
                     ])
 
+    if fsvernum < 6:
+        ar3_wf.connect([(inputspec, wm_parcellation, [('filled', 'filled')])])
+
     # White Matter Segmentation Stats
 
     wm_segstats = pe.Node(SegStatsReconAll(), name="WM_Segmentation_Statistics")