From 6e18fceed7fc1d6ce1026f787696d9df9e605232 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@gmail.com>
Date: Wed, 10 Oct 2018 14:04:32 +0100
Subject: [PATCH] BUG: don't include unset variables in all_variables

---
 fsl/utils/filetree/filetree.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/fsl/utils/filetree/filetree.py b/fsl/utils/filetree/filetree.py
index 151583e30..edcccc9fb 100644
--- a/fsl/utils/filetree/filetree.py
+++ b/fsl/utils/filetree/filetree.py
@@ -48,10 +48,11 @@ class FileTree(object):
         """
         All tree variables including those from the parent tree
         """
+        without_none = {key: value for key, value in self.variables.items() if value is not None}
         if self.parent is None:
-            return dict(self.variables)
+            return without_none
         res = self.parent.all_variables
-        res.update(self.variables)
+        res.update(without_none)
         return res
 
     def get_variable(self, name: str) -> str:
-- 
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