diff --git a/matlab/global_initialization.m b/matlab/global_initialization.m
index 4c9d8c7981d11a48a940611d798a5c25b8ce200d..e9b3b320867593719b70e953b1f50f0b179eb46e 100644
--- a/matlab/global_initialization.m
+++ b/matlab/global_initialization.m
@@ -125,8 +125,15 @@ M_.osr.variable_weights=[];
 M_.osr.variable_indices =[];
 
 M_.instr_id=[];
-% Set default options_ in function below; this change was made for the GUI
-options_ = default_option_values(M_);
+
+% Set default options_ but keep global_init_file field if defined in the driver.
+if isstruct(options_) && isfield(options_, 'global_init_file')
+    global_init_file = options_.global_init_file;
+    options_ = default_option_values(M_);
+    options_.global_init_file = global_init_file;
+else
+    options_ = default_option_values(M_);
+end
 
 % initialize persistent variables in priordens()
 priordens([],[],[],[],[],[],1);