FIX: Allows for changing of RB atlas

Author: David Ellis

nipype/workflows/smri/freesurfer/recon.py

@@ -146,6 +146,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         stop = 0.0001
         exvivo = True
         entorhinal = True
+        rb_date = "2014-08-21"
     else:
         # 5.3 is default
         if 'v5.3' in fs_version_full:
@@ -161,6 +162,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         stop = None
         exvivo = False
         entorhinal = False
+        rb_date = "2008-03-26"
 
     print("FreeSurfer Version: {0}".format(fs_version))
 
@@ -179,7 +181,8 @@ def setconfig(reg_template=None,
                   color_table=None,
                   lookup_table=None,
                   wm_lookup_table=None,
-                  awk_file=None):
+                  awk_file=None,
+                  rb_date=rb_date):
         """Set optional configurations to the default"""
         from nipype.workflows.smri.freesurfer.utils import getdefaultconfig
         def checkarg(arg, default):
@@ -188,7 +191,7 @@ def checkarg(arg, default):
                 return arg
             else:
                 return default
-        defaultconfig = getdefaultconfig(exitonfail=True)
+        defaultconfig = getdefaultconfig(exitonfail=True, rb_date=rb_date)
         # set the default template and classifier files
         reg_template = checkarg(reg_template, defaultconfig['registration_template'])
         reg_template_withskull = checkarg(reg_template_withskull,

nipype/workflows/smri/freesurfer/utils.py

@@ -420,7 +420,7 @@ def mkdir_p(path):
         else:
             raise
 
-def getdefaultconfig(exitonfail=False):
+def getdefaultconfig(exitonfail=False, rb_date="2014-08-21"):
     config = { 'custom_atlas' : None,
                'cw256' : False,
                'field_strength' : '1.5T',
@@ -440,9 +440,9 @@ def getdefaultconfig(exitonfail=False):
     config['awk_file'] = os.path.join(config['fs_home'], 'bin',
                                       'extract_talairach_avi_QA.awk')
     config['registration_template'] = os.path.join(config['fs_home'], 'average',
-                                                   'RB_all_2014-08-21.gca')
+                                                   'RB_all_{0}.gca'.format(rb_date))
     config['registration_template_withskull'] = os.path.join(config['fs_home'], 'average',
-                                                             'RB_all_withskull_2014-08-21.gca')
+                                                             'RB_all_withskull_{0}.gca'.format(rb_date))
     for hemi in ('lh', 'rh'):
         config['{0}_atlas'.format(hemi)] = os.path.join(
             config['fs_home'], 'average',