ENH: Makes mris_make_surfaces compatable with the 5.3 recon-all.

Author: David Ellis

nipype/interfaces/freesurfer/utils.py

@@ -1902,6 +1902,8 @@ class MakeSurfacesInputSpec(FSTraitedSpec):
         argstr="-max %.1f", desc="No documentation (used for longitudinal processing)")
     longitudinal = traits.Bool(
         argstr="-long", desc="No documentation (used for longitudinal processing)")
+    white = traits.String(argstr="-white %s",
+                          desc="White surface name")
     copy_inputs = traits.Bool(mandatory=False,
                               desc="If running as a node, set this to True." +
                               "This will copy the input files to the node " +
@@ -1958,13 +1960,11 @@ def run(self, **inputs):
                          folder='mri', basename='filled.mgz')
             for originalfile in [self.inputs.in_aseg,
                                  self.inputs.in_T1]:
-                if isdefined(originalfile):
-                    copy2subjdir(self, originalfile, folder='mri')
+                copy2subjdir(self, originalfile, folder='mri')
             for originalfile in [self.inputs.orig_white,
                                  self.inputs.orig_pial,
                                  self.inputs.in_orig]:
-                if isdefined(originalfile):
-                    copy2subjdir(self, originalfile, folder='surf')
+                copy2subjdir(self, originalfile, folder='surf')
             if isdefined(self.inputs.in_label):
                 copy2subjdir(self, self.inputs.in_label, 'label',
                              '{0}.aparc.annot'.format(self.inputs.hemisphere))
@@ -1981,9 +1981,11 @@ def _format_arg(self, name, spec, value):
             basename = os.path.basename(value)
             # whent the -mgz flag is specified, it assumes the mgz extension
             if self.inputs.mgz:
-                prefix = basename.rstrip('.mgz')
+                prefix = value.rstrip('.mgz')
             else:
                 prefix = basename
+            if prefix == 'aseg':
+                return # aseg is already the default
             return spec.argstr % prefix
         elif name in ['orig_white', 'orig_pial']:
             # these inputs do take full file paths or even basenames
@@ -2038,7 +2040,7 @@ def _list_outputs(self):
 
 class CurvatureInputSpec(FSTraitedSpec):
     in_file = File(argstr="%s", position=-2, mandatory=True, exists=True,
-                   desc="Input file for Curvature")
+                   copyfile=True, desc="Input file for Curvature")
     # optional
     threshold = traits.Float(
         argstr="-thresh %.3f", mandatory=False, desc="Undocumented input threshold")
@@ -2082,7 +2084,6 @@ def _format_arg(self, name, spec, value):
         if self.inputs.copy_input:
             if name == 'in_file':
                 basename = os.path.basename(value)
-                shutil.copy(value, basename)
                 return spec.argstr % basename
         return super(Curvature, self)._format_arg(name, spec, value)
 

nipype/workflows/smri/freesurfer/autorecon2.py

@@ -156,8 +156,14 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
     else:
         ca_register.inputs.levels = 2
         ca_register.inputs.A = 1
-        ar2_wf.connect([(ar1_inputs, ca_register, [('template_talairach_m3z', 'l_files')])])
+        ar2_wf.connect([(inputspec, ca_register, [('template_talairach_m3z', 'l_files')])])
 
+
+    if fsvernum < 6:
+        # 5.3 runs two ca_register steps
+        ca_register2 = pe.Node(CARegister(), name='CA_Register2')
+        ca_register2.inputs.invert_and_save = True
+        ar2_wf.connect(ca_register, 'out_file', ca_register2, '')
     # Remove Neck
     """
     The neck region is removed from the NU-corrected volume mri/nu.mgz. Makes use
@@ -248,7 +254,10 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
                                ['out_file'],
                                copy_file),
                       name='Copy_CCSegmentation')
-    copy_cc.inputs.out_file = 'aseg.presurf.mgz'
+    if fsvernum > 6:
+        copy_cc.inputs.out_file = 'aseg.presurf.mgz'
+    else:
+        copy_cc.inputs.out_file = 'aseg.mgz'
 
     ar2_wf.connect([(segment_cc, copy_cc, [('out_file', 'in_file')])
                     ])

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -166,11 +166,19 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         # Pial Surface
 
         ar3_pial = pe.Node(MakeSurfaces(), name="Make_Pial_Surface")
-        ar3_pial.inputs.no_white = True
         ar3_pial.inputs.mgz = True
         ar3_pial.inputs.hemisphere = hemisphere
         ar3_pial.inputs.copy_inputs = True
 
+
+        if fsvernum < 6:
+            hemi_wf.connect(hemi_inputspec1, 'white', ar3_pial, 'in_white')
+            ar3_pial.inputs.white = 'NOWRITE'
+        else:
+            ar3_pial.inputs.no_white = True
+            hemi_wf.connect([(hemi_inputspec1, ar3_pial, [('white', 'orig_pial'),
+                                                          ('white', 'orig_white')])])
+
         hemi_wf.connect([(hemi_inputspec1, ar3_pial, [('wm', 'in_wm'),
                                                       ('orig', 'in_orig'),
                                                       ('filled', 'in_filled'),
@@ -603,13 +611,17 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
 
     if fsvernum > 6:
         apas_2_aseg = pe.Node(Apas2Aseg(), name="Apas_2_Aseg")
+        ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')])])        
     else:
-        apas_2_aseg = pe.Node(Function(['in_file', 'out_file'],
+        # aseg.mgz gets edited in place, so we'll copy and pass it to the
+        # outputspec once aparc_2_aseg has completed
+        def out_aseg(in_aparcaseg, in_aseg, out_file):
+            out_file = copy_file(in_aseg, out_file)
+            return out_file
+        apas_2_aseg = pe.Node(Function(['in_aparcaseg', 'in_aseg', 'out_file'],
                                        ['out_file'],
-                                       copy_file),
-                              name="Copy2Aseg")
-        
-    ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')])])        
+                                       out_aseg),
+                              name="Aseg")
     apas_2_aseg.inputs.out_file = "aseg.mgz"