diff --git a/fsl/utils/filetree/utils.py b/fsl/utils/filetree/utils.py
index e7dd4aad3347c678e32217e09eecf33d2ecdee35..0b82929491c9a8994d252f24704f66dff87f8411 100644
--- a/fsl/utils/filetree/utils.py
+++ b/fsl/utils/filetree/utils.py
@@ -158,6 +158,7 @@ def extract_variables(template, filename, known_vars=None):
         ))
         while '//' in sub_re:
             sub_re = sub_re.replace('//', '/')
+        sub_re = sub_re.replace('.', '\.')
         if re.match(sub_re, filename) is None:
             continue