diff --git a/matlab/ms-sbvar/ms_compute_mdd.m b/matlab/ms-sbvar/ms_compute_mdd.m
index 4874a8344..e92061359 100644
--- a/matlab/ms-sbvar/ms_compute_mdd.m
+++ b/matlab/ms-sbvar/ms_compute_mdd.m
@@ -80,5 +80,4 @@ if exist(mdd_filename,'file')
     oo_.ms.mueller_log_mdd = muller_mdd;
     oo_.ms.bridged_log_mdd = bridge_mdd;
 end
-options_ = initialize_ms_sbvar_options(M_, options_);
 end
diff --git a/matlab/ms-sbvar/ms_compute_probabilities.m b/matlab/ms-sbvar/ms_compute_probabilities.m
index 51c6b6d08..a4a5dcb4c 100644
--- a/matlab/ms-sbvar/ms_compute_probabilities.m
+++ b/matlab/ms-sbvar/ms_compute_probabilities.m
@@ -61,5 +61,4 @@ if ischar(prob_out_file)
     computed_probabilities = load(prob_out_file);
     plot_ms_probabilities(computed_probabilities,options_);
 end
-options_ = initialize_ms_sbvar_options(M_, options_);
 end
diff --git a/matlab/ms-sbvar/ms_estimation.m b/matlab/ms-sbvar/ms_estimation.m
index b14943968..c591f4f98 100644
--- a/matlab/ms-sbvar/ms_estimation.m
+++ b/matlab/ms-sbvar/ms_estimation.m
@@ -70,5 +70,4 @@ mexErrCheck('ms_estimation', err);
 [err, oo_.ms.A0, oo_.ms.Aplus, oo_.ms.Zeta, oo_.ms.Q] = ...
     mex_ms_convert_free_parameters(options_.ms.estimation_file_tag, oo_.ms.maxparams);
 mexErrCheck('mex_ms_convert_free_parameters', err);
-options_ = initialize_ms_sbvar_options(M_, options_);
 end
diff --git a/matlab/ms-sbvar/ms_forecast.m b/matlab/ms-sbvar/ms_forecast.m
index 7619a1aea..67fbe4eb1 100644
--- a/matlab/ms-sbvar/ms_forecast.m
+++ b/matlab/ms-sbvar/ms_forecast.m
@@ -66,5 +66,4 @@ if exist(options_.ms.mh_file,'file') > 0
     mexErrCheck('mex_ms_forecast bayesian regimes ', err);
     save([forecastdir filesep 'bayesian_forecast.mat'], 'forecast', 'regime_forecast');
 end
-options_ = initialize_ms_sbvar_options(M_, options_);
 end
diff --git a/matlab/ms-sbvar/ms_irf.m b/matlab/ms-sbvar/ms_irf.m
index 1ae637810..a3fa4c730 100644
--- a/matlab/ms-sbvar/ms_irf.m
+++ b/matlab/ms-sbvar/ms_irf.m
@@ -75,5 +75,4 @@ if exist(options_.ms.mh_file,'file') > 0
     end
     save([irfdir filesep 'bayesian_irf.mat'], 'irf', 'regime_irfs');
 end
-options_ = initialize_ms_sbvar_options(M_, options_);
 end
diff --git a/matlab/ms-sbvar/ms_simulation.m b/matlab/ms-sbvar/ms_simulation.m
index 2a91abf57..c7f141970 100644
--- a/matlab/ms-sbvar/ms_simulation.m
+++ b/matlab/ms-sbvar/ms_simulation.m
@@ -48,6 +48,4 @@ opt = [opt ' -mh ' num2str(options_.ms.adaptive_mh_draws)];
 % simulation
 [err] = ms_sbvar_command_line(opt);
 mexErrCheck('ms_simulation',err);
-
-options_ = initialize_ms_sbvar_options(M_, options_);
 end
diff --git a/matlab/ms-sbvar/ms_variance_decomposition.m b/matlab/ms-sbvar/ms_variance_decomposition.m
index 3a66fbe75..74a36e54e 100644
--- a/matlab/ms-sbvar/ms_variance_decomposition.m
+++ b/matlab/ms-sbvar/ms_variance_decomposition.m
@@ -66,5 +66,4 @@ if exist(options_.ms.mh_file,'file') > 0
     mexErrCheck('mex_ms_variance_decomposition bayesian regimes ', err);
     save([vddir filesep 'bayesian_vd.mat'], 'vd', 'regime_vd');
 end
-options_ = initialize_ms_sbvar_options(M_, options_);
 end
diff --git a/preprocessor/ComputingTasks.cc b/preprocessor/ComputingTasks.cc
index d4b9b92fb..c588060b5 100644
--- a/preprocessor/ComputingTasks.cc
+++ b/preprocessor/ComputingTasks.cc
@@ -942,6 +942,7 @@ MSSBVAREstimationStatement::checkPass(ModFileStructure &mod_file_struct)
 void
 MSSBVAREstimationStatement::writeOutput(ostream &output, const string &basename) const
 {
+  output << "options_ = initialize_ms_sbvar_options(M_, options_);" << endl;
   options_list.writeOutput(output);
   output << "[options_, oo_] = ms_estimation(M_, options_, oo_);" << endl;
 }
@@ -960,6 +961,7 @@ MSSBVARSimulationStatement::checkPass(ModFileStructure &mod_file_struct)
 void
 MSSBVARSimulationStatement::writeOutput(ostream &output, const string &basename) const
 {
+  output << "options_ = initialize_ms_sbvar_options(M_, options_);" << endl;
   options_list.writeOutput(output);
   output << "[options_, oo_] = ms_simulation(M_, options_, oo_);" << endl;
 }
@@ -978,6 +980,7 @@ MSSBVARComputeMDDStatement::checkPass(ModFileStructure &mod_file_struct)
 void
 MSSBVARComputeMDDStatement::writeOutput(ostream &output, const string &basename) const
 {
+  output << "options_ = initialize_ms_sbvar_options(M_, options_);" << endl;
   options_list.writeOutput(output);
   output << "[options_, oo_] = ms_compute_mdd(M_, options_, oo_);" << endl;
 }
@@ -996,6 +999,7 @@ MSSBVARComputeProbabilitiesStatement::checkPass(ModFileStructure &mod_file_struc
 void
 MSSBVARComputeProbabilitiesStatement::writeOutput(ostream &output, const string &basename) const
 {
+  output << "options_ = initialize_ms_sbvar_options(M_, options_);" << endl;
   options_list.writeOutput(output);
   output << "[options_, oo_] = ms_compute_probabilities(M_, options_, oo_);" << endl;
 }
@@ -1016,6 +1020,7 @@ MSSBVARIrfStatement::checkPass(ModFileStructure &mod_file_struct)
 void
 MSSBVARIrfStatement::writeOutput(ostream &output, const string &basename) const
 {
+  output << "options_ = initialize_ms_sbvar_options(M_, options_);" << endl;
   symbol_list.writeOutput("var_list_", output);
   options_list.writeOutput(output);
   output << "[options_, oo_] = ms_irf(var_list_,M_, options_, oo_);" << endl;
@@ -1035,6 +1040,7 @@ MSSBVARForecastStatement::checkPass(ModFileStructure &mod_file_struct)
 void
 MSSBVARForecastStatement::writeOutput(ostream &output, const string &basename) const
 {
+  output << "options_ = initialize_ms_sbvar_options(M_, options_);" << endl;
   options_list.writeOutput(output);
   output << "[options_, oo_] = ms_forecast(M_, options_, oo_);" << endl;
 }
@@ -1053,6 +1059,7 @@ MSSBVARVarianceDecompositionStatement::checkPass(ModFileStructure &mod_file_stru
 void
 MSSBVARVarianceDecompositionStatement::writeOutput(ostream &output, const string &basename) const
 {
+  output << "options_ = initialize_ms_sbvar_options(M_, options_);" << endl;
   options_list.writeOutput(output);
   output << "[options_, oo_] = ms_variance_decomposition(M_, options_, oo_);" << endl;
 }