diff --git a/src/mvesuvio/analysis_fitting.py b/src/mvesuvio/analysis_fitting.py
index fe41ac01..3f25a8a7 100644
--- a/src/mvesuvio/analysis_fitting.py
+++ b/src/mvesuvio/analysis_fitting.py
@@ -128,8 +128,8 @@ def subtractAllMassesExceptFirst(ic, ws, ncpForEachMass):
 
     wsSubMass = CloneWorkspace(InputWorkspace=ws, OutputWorkspace=ws.name() + "_Mass0")
     passDataIntoWS(dataX, dataY, dataE, wsSubMass)
-    # MaskDetectors(Workspace=wsSubMass, WorkspaceIndexList=ic.maskedDetectorIdx)
-    MaskDetectors(Workspace=wsSubMass, SpectraList=ic.maskedSpecAllNo)
+    wsMask, maskList = ExtractMask(ws)
+    MaskDetectors(Workspace=wsSubMass, MaskedWorkspace=wsMask)
     SumSpectra(
         InputWorkspace=wsSubMass.name(), OutputWorkspace=wsSubMass.name() + "_Sum"
     )
diff --git a/src/mvesuvio/main/run_routine.py b/src/mvesuvio/main/run_routine.py
index 90b4417a..99be5f6d 100644
--- a/src/mvesuvio/main/run_routine.py
+++ b/src/mvesuvio/main/run_routine.py
@@ -58,6 +58,10 @@ def setup(self):
         self.input_ws_path =  self.experiment_path / "input_ws"
         self.input_ws_path.mkdir(parents=True, exist_ok=True)
 
+        # TODO: Output paths should probably not be set like this 
+        self._set_output_paths(self.bckwdIC) 
+        self._set_output_paths(self.fwdIC) 
+
         # TODO: remove this by fixing circular import 
         self.fwdIC.name = name_for_starting_ws(self.fwdIC)
         self.bckwdIC.name = name_for_starting_ws(self.bckwdIC)
@@ -227,9 +231,6 @@ def _create_analysis_algorithm(self, load_ai, ai):
 
         ipFilesPath = Path(handle_config.read_config_var("caching.ipfolder"))
 
-        # TODO: Output paths should probably not be set here
-        self._set_output_paths(ai) 
-
         kwargs = {
             "InputWorkspace": cropedWs.name(),
             "InputProfiles": profiles_table.name(),