diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index da06a5c574..66e3c5904d 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1160,7 +1160,7 @@ def _list_outputs(self):
                 if suffix.endswith('.txt'):
                     change_ext = False
                 if isdefined(inval):
-                    outputs[key] = inval
+                    outputs[key] = os.path.abspath(inval)
                 else:
                     outputs[key] = self._gen_fname(
                         self.inputs.in_file,