AFNI issue

Author: mick-d

nipype/interfaces/base.py

@@ -1469,6 +1469,23 @@ def _filename_from_source(self, name):
             if trait_spec.keep_extension and ext:
                 return retval
             return self._overload_extension(retval)
+        elif isdefined(retval):
+            if "%s" in retval:
+                if isinstance(trait_spec.name_source, list):
+                    for ns in trait_spec.name_source:
+                        if isdefined(getattr(self.inputs, ns)):
+                            name_source = ns
+                            break
+                else:
+                    name_source = trait_spec.name_source
+                if name_source.endswith(os.path.sep):
+                    name_source = name_source[:-len(os.path.sep)]
+                _, base, _ = split_filename(getattr(self.inputs, name_source))
+                retval = os.path.abspath(retval % base)
+            _, _, ext = split_filename(retval)
+            if trait_spec.keep_extension and ext:
+                return retval
+            return self._overload_extension(retval)
         return retval
 
     def _gen_filename(self, name):