FIX: Fixes issues with incorrectly formatting strings.

Author: ellisdg

nipype/workflows/smri/freesurfer/autorecon1.py

@@ -345,7 +345,7 @@ def awkfile(in_file, log_file):
             """
             import subprocess
             import os
-            command = ['awk', '-f', awk_file, log_file]
+            command = ['awk', '-f', in_file, log_file]
             print(''.join(command))
             subprocess.call(command)
             log_file = os.path.abspath(log_file)
@@ -405,7 +405,6 @@ def awkfile(in_file, log_file):
                                                    ['out_file'],
                                                    copy_file),
                                           name='Copy_Template_Brainmask')
-        #TODO: Change this to inputspec
         copy_template_brainmask.inputs.out_file = 'brainmask_{0}.mgz'.format(config['long_template'])
 
         ar1_wf.connect([(inputspec, copy_template_brainmask, [('template_brainmask', 'in_file')])])

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -467,7 +467,7 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None):
         hemiwf2.connect([(hemi_inputspec2, contrast, [('orig_mgz', 'orig'),
                                                       ('rawavg', 'rawavg'),
                                                       ('{0}_white'.format(hemisphere), 'white'),
-                                                      ('cortex_label'.format(hemisphere), 'cortex'),
+                                                      ('cortex_label', 'cortex'),
                                                       ('aparc_annot', 'annotation'),
                                                       ('thickness', 'thickness'),
                                                       ]),

nipype/workflows/smri/freesurfer/utils.py

@@ -448,7 +448,7 @@ def getdefaultconfig():
             '{0}.average.curvature.filled.buckner40.tif'.format(hemi))
         config['{0}_classifier'.format(hemi)] = os.path.join(
             config['fs_home'], 'average',
-            'rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs'.format(hemi))
+            '{0}.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs'.format(hemi))
         config['{0}_classifier2'.format(hemi)] = os.path.join(
             config['fs_home'], 'average',
             '{0}.destrieux.simple.2009-07-29.gcs'.format(hemi))