FIX: Adds stop and shrink values to autorecon2.py to ensure that the

6.0beta still works.

Author: David Ellis

nipype/workflows/smri/freesurfer/autorecon1.py

@@ -36,7 +36,7 @@ def checkT1s(T1_files, cw256=False):
     return T1_files, cw256, resample_type, origvol_names
 
 def create_AutoRecon1(name="AutoRecon1", longitudinal=False, distance=200,
-                      custom_atlas=None, plugin_args=None, shrink=2, stop=0.0001,
+                      custom_atlas=None, plugin_args=None, shrink=None, stop=None,
                       fsvernum=5.3):
     """Creates the AutoRecon1 workflow in nipype.
 

nipype/workflows/smri/freesurfer/autorecon2.py

@@ -11,7 +11,8 @@ def copy_ltas(in_file, subjects_dir, subject_id, long_template):
     return out_file
 
 def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
-                      plugin_args=None, fsvernum=5.3):
+                      plugin_args=None, fsvernum=5.3,
+                          stop=None, shrink=None):
     # AutoRecon2
     # Workflow
     ar2_wf = pe.Workflow(name=name)

nipype/workflows/smri/freesurfer/recon.py

@@ -259,7 +259,8 @@ def checkarg(arg, default):
                                               'inputspec.reg_template_withskull'),
                                              ('awk_file', 'inputspec.awk_file')])])
     # create AutoRecon2
-    ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args, fsvernum=fsvernum)
+    ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args, fsvernum=fsvernum,
+                                            stop=stop, shrink=shrink)
     # connect inputs for AutoRecon2
     reconall.connect([(inputspec, ar2_wf, [('num_threads', 'inputspec.num_threads')]),
                       (config_node, ar2_wf, [('reg_template_withskull',