automatically set ANTSPATH when possible

Author: oesteban

nipype/interfaces/ants/segmentation.py

@@ -14,7 +14,8 @@
 import os
 from ...external.due import BibTeX
 from ...utils.filemanip import split_filename, copyfile
-from ..base import TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined
+from ..base import (TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined,
+                    _exists_in_path)
 from .base import ANTSCommand, ANTSCommandInputSpec
 
 
@@ -693,20 +694,22 @@ class BrainExtraction(ANTSCommand):
     _cmd = 'antsBrainExtraction.sh'
 
     def _run_interface(self, runtime, correct_return_codes=(0,)):
+        # antsBrainExtraction.sh requires ANTSPATH to be defined
         out_environ = self._get_environ()
         if out_environ.get('ANTSPATH') is None:
             runtime.environ.update(out_environ)
             executable_name = self.cmd.split()[0]
-            exist_val, cmd_path = _exists_in_path(executable_name,
-                                                  runtime.environ)
+            exist_val, cmd_path = _exists_in_path(executable_name, runtime.environ)
             if not exist_val:
                 raise IOError("command '%s' could not be found on host %s" %
                               (self.cmd.split()[0], runtime.hostname))
 
-            runtime.environ.update({'ANTSPATH': cmd_path})
+            # Set the environment variable if found
+            runtime.environ.update({'ANTSPATH': os.path.dirname(cmd_path)})
 
         runtime = super(BrainExtraction, self)._run_interface(runtime)
 
+        # Still, double-check if it didn't found N4
         if 'we cant find the N4 program' in runtime.stdout:
             errmsg = ('antsBrainExtraction.sh requires the environment variable '
                       'ANTSPATH to be defined')