diff --git a/fsl/utils/filetree/filetree.py b/fsl/utils/filetree/filetree.py
index cbd8673dd79bd8a973990bd3ccab9f4a792e9b20..12cfc5a6990ab33f98ea2fd363df3d32ff93541b 100644
--- a/fsl/utils/filetree/filetree.py
+++ b/fsl/utils/filetree/filetree.py
@@ -394,7 +394,7 @@ class FileTree(object):
         self.variables = {}
 
     @classmethod
-    def read(cls, tree_name: str, directory='.', partial_fill=True, **variables) -> "FileTree":
+    def read(cls, tree_name: str, directory='.', partial_fill=False, **variables) -> "FileTree":
         """
         Reads a FileTree from a specific file
 
diff --git a/fsl/utils/filetree/query.py b/fsl/utils/filetree/query.py
index a2e215c848558f304e62c61ba529614bd05038f0..d371bcdf37a7d31d7ed333e602ba50f992477ade 100644
--- a/fsl/utils/filetree/query.py
+++ b/fsl/utils/filetree/query.py
@@ -89,6 +89,8 @@ class FileTreeQuery(object):
 
         :arg tree: The :class:`.FileTree` object
         """
+        # Hard-code into the templates any pre-defined variables
+        tree = tree.partial_fill()
 
         # Find all files present in the directory
         # (as Match objects), and find all variables,
diff --git a/tests/test_filetree/test_read.py b/tests/test_filetree/test_read.py
index 8382cc6d2f48a3965a7e71ca52c4708e8f06ecb9..bb4ad67e33d44ab6c9b4599eae69206015940fe2 100644
--- a/tests/test_filetree/test_read.py
+++ b/tests/test_filetree/test_read.py
@@ -14,14 +14,21 @@ def same_path(p1, p2):
 
 def test_simple_tree():
     tree = filetree.FileTree.read('eddy')
-    assert 'basename' not in tree.variables
+    assert 'basename' in tree.variables
 
     same_path(tree.get('basename'), './eddy_output')
     same_path(tree.get('image'), './eddy_output.nii.gz')
+    same_path(tree.update(basename='eddy').get('image'), './eddy.nii.gz')
 
     tree = filetree.FileTree.read('eddy.tree', basename='out')
+    assert 'basename' in tree.variables
+    same_path(tree.get('basename'), './out')
+    same_path(tree.update(basename='eddy').get('image'), './eddy.nii.gz')
+
+    tree = filetree.FileTree.read('eddy.tree', basename='out', partial_fill=True)
     assert 'basename' not in tree.variables
     same_path(tree.get('basename'), './out')
+    same_path(tree.update(basename='eddy').get('image'), './out.nii.gz')
 
     with pytest.raises(ValueError):
         filetree.FileTree.read('non_existing')