diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py
index 2f8b432bb3..1d209c3022 100644
--- a/nipype/interfaces/freesurfer/preprocess.py
+++ b/nipype/interfaces/freesurfer/preprocess.py
@@ -628,10 +628,17 @@ class ReconAllInputSpec(CommandLineInputSpec):
                        argstr="-hemi %s")
     T1_files = InputMultiPath(File(exists=True), argstr='-i %s...',
                               desc='name of T1 file to process')
-    T2_file = File(exists=True, argstr="-T2 %s", min_ver='5.3.0',
+    T2_file = File(exists=True, argstr="-T2 %s",
+                   min_ver='5.3.0',
                    desc='Convert T2 image to orig directory')
-    use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0',
-                         desc='Use converted T2 to refine the cortical surface')
+    FLAIR_file = File(exists=True, argstr="-FLAIR %s",
+                      min_ver='5.3.0',
+                      desc='Convert FLAIR image to orig directory')
+    use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0', xor=['use_FLAIR'],
+                         desc='Use T2 image to refine the pial surface')
+    use_FLAIR = traits.Bool(argstr="-FLAIRpial",
+                            min_ver='5.3.0', xor=['use_T2'],
+                            desc='Use FLAIR image to refine the pial surface')
     openmp = traits.Int(argstr="-openmp %d",
                         desc="Number of processors to use in parallel")
     parallel = traits.Bool(argstr="-parallel",
diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
index d02b2b47df..f823855333 100644
--- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
+++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
@@ -4,7 +4,10 @@
 
 
 def test_ReconAll_inputs():
-    input_map = dict(T1_files=dict(argstr='-i %s...',
+    input_map = dict(FLAIR_file=dict(argstr='-FLAIR %s',
+    min_ver='5.3.0',
+    ),
+    T1_files=dict(argstr='-i %s...',
     ),
     T2_file=dict(argstr='-T2 %s',
     min_ver='5.3.0',
@@ -108,8 +111,13 @@ def test_ReconAll_inputs():
     terminal_output=dict(deprecated='1.0.0',
     nohash=True,
     ),
+    use_FLAIR=dict(argstr='-FLAIRpial',
+    min_ver='5.3.0',
+    xor=['use_T2'],
+    ),
     use_T2=dict(argstr='-T2pial',
     min_ver='5.3.0',
+    xor=['use_FLAIR'],
     ),
     xopts=dict(argstr='-xopts-%s',
     ),