fixing wrong output directory in afni base gen_filename

Author: bpinsard

nipype/interfaces/afni/base.py

@@ -214,9 +214,10 @@ def _gen_filename(self, name):
 
             _, base, _ = split_filename(
                 getattr(self.inputs, trait_spec.name_source))
-            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd='')
+            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd=os.getcwd())
         else:
-            return super(AFNICommand, self)._gen_filename(name)
+            return os.path.join(os.getcwd(),
+                                super(AFNICommand, self)._gen_filename(name))
 
     def _overload_extension(self, value):
         path, base, _ = split_filename(value)