diff --git a/src/pyMBIR_UI/recon_HFIR_script_batch.py b/src/pyMBIR_UI/recon_HFIR_script_batch.py
old mode 100644
new mode 100755
index f4644c7..032fbea
--- a/src/pyMBIR_UI/recon_HFIR_script_batch.py
+++ b/src/pyMBIR_UI/recon_HFIR_script_batch.py
@@ -153,11 +153,15 @@ def main():
     #pg.image(rec_mbir);
     #pg.QtGui.QApplication.exec_()
     if input_dict["write_op"] == True:
-        dxchange.write_tiff_stack(rec_mbir, fname=input_dict["op_path"], start=z_start, overwrite=True)
+        print(f"input_dict['op_path']: {input_dict['op_path']}")
+        temp_path = os.path.join(input_dict['op_path'], "mbir")
+        dxchange.write_tiff_stack(rec_mbir, fname=temp_path, start=z_start, overwrite=True)
 
     # when done write stop file in batch mode
-    #if input_dict["running_mode"] == "batch":
-    #    with open(STOP_FILE_NAME
+    if input_dict["running_mode"] == "batch":
+        with open(STOP_FILE_NAME, 'w') as json_file:
+            json.dump({"stop": True}, json_file)
+
 
 if __name__ == "__main__":
     main()
diff --git a/src/pyMBIR_UI/reconstruction_launcher.py b/src/pyMBIR_UI/reconstruction_launcher.py
index 8fb5403..1c8eb19 100644
--- a/src/pyMBIR_UI/reconstruction_launcher.py
+++ b/src/pyMBIR_UI/reconstruction_launcher.py
@@ -141,18 +141,19 @@ def run(self):
         # for debugging only !!! remove me
         #dictionary_of_arguments['n_vox_z'] = 6
 
-
-
-
-
         base_output_folder = os.path.basename(dictionary_of_arguments['data_path'])
-        full_output_folder = os.path.join(dictionary_of_arguments['op_path'], base_output_folder +
-                                          "_pymbir_reconstructed")
-        dictionary_of_arguments['op_path'] = full_output_folder
+        full_output_folder = os.path.join(dictionary_of_arguments['op_path'])
+
+ #       full_output_folder = os.path.join(dictionary_of_arguments['op_path'], base_output_folder +
+ #                                         "_pymbir_reconstructed")
+#        dictionary_of_arguments['op_path'] = full_output_folder
         logging.info(f"Final image will be output in {full_output_folder}")
         make_or_reset_folder(dictionary_of_arguments['op_path'])
         logging.info(f"Reset output folder: {full_output_folder}")
 
+        dictionary_of_arguments['temp_op_dir'] = os.path.join(dictionary_of_arguments['op_path'], "temporary_pymbir_reconstructed")
+        make_or_reset_folder(dictionary_of_arguments['temp_op_dir'])
+
         logging.info(f"-> Dictionary of arguments: {dictionary_of_arguments}")
 
         logging.info(f"-> reset temporary folder: {dictionary_of_arguments['temp_op_dir']}")
@@ -167,7 +168,7 @@ def run(self):
 
         logging.info(f"-> Saving config file to be called from command line script")
         home_folder = os.path.expanduser("~")
-        json_file_name = os.path.join(home_folder, "config_batch_mode.json" )
+        json_file_name = os.path.join(home_folder, "config_batch_mode.json")
         with open(json_file_name, 'w') as json_file:
             json.dump(dictionary_of_arguments, json_file)
 
@@ -296,9 +297,14 @@ def check_output_file(self):
         o_event.update_output_plot()
 
     def check_output_3d_volume(self):
-        output_folder = self.dictionary_of_arguments["op_path"]
+        print("in check 3D")
+        base_output_folder = os.path.basename(self.dictionary_of_arguments['data_path'])
+        output_folder = self.dictionary_of_arguments['op_path']
+        print(f"output_folder: {output_folder}")
         list_tiff_files_in_output_folder = glob.glob(os.path.join(output_folder, "*.tif?"))
+        print(f"list tiff:{list_tiff_files_in_output_folder}")
         number_of_files_in_output_folder = len(list_tiff_files_in_output_folder)
+        print(f"number of files: {number_of_files_in_output_folder}")
         if number_of_files_in_output_folder == 0:
             self.parent.ui.tabWidget_3.setTabEnabled(1, False)
             return