diff --git a/Detectors/MUON/MCH/Align/src/AlignmentSpec.cxx b/Detectors/MUON/MCH/Align/src/AlignmentSpec.cxx
index 948ac1bda9117..8a1df9c98bb9b 100644
--- a/Detectors/MUON/MCH/Align/src/AlignmentSpec.cxx
+++ b/Detectors/MUON/MCH/Align/src/AlignmentSpec.cxx
@@ -208,11 +208,21 @@ class AlignmentTask
 
     auto doEvaluation = ic.options().get<bool>("do-evaluation");
     mAlign.SetDoEvaluation(doEvaluation);
+
     // Variation range for parameters
-    mAlign.SetAllowedVariation(0, 2.0);
-    mAlign.SetAllowedVariation(1, 0.3);
-    mAlign.SetAllowedVariation(2, 0.002);
-    mAlign.SetAllowedVariation(3, 2.0);
+    auto AllowX = ic.options().get<float>("variation-x");
+    auto AllowY = ic.options().get<float>("variation-y");
+    auto AllowPhi = ic.options().get<float>("variation-phi");
+    auto AllowZ = ic.options().get<float>("variation-z");
+    mAlign.SetAllowedVariation(0, AllowX);
+    mAlign.SetAllowedVariation(1, AllowY);
+    mAlign.SetAllowedVariation(2, AllowPhi);
+    mAlign.SetAllowedVariation(3, AllowZ);
+
+    // Sigma XY
+    auto SigmaX = ic.options().get<float>("sigma-x");
+    auto SigmaY = ic.options().get<float>("sigma-y");
+    mAlign.SetSigmaXY(SigmaX, SigmaY);
 
     // Configuration for track fitter
     const auto& trackerParam = TrackerParam::Instance();
@@ -223,14 +233,28 @@ class AlignmentTask
     mImproveCutChi2 = 2. * trackerParam.sigmaCutForImprovement * trackerParam.sigmaCutForImprovement;
 
     // Fix chambers
-    auto input_fixchambers = ic.options().get<string>("fix-chamber");
-    std::stringstream string_chambers(input_fixchambers);
-    string_chambers >> std::ws;
-    while (string_chambers.good()) {
-      string substr;
-      std::getline(string_chambers, substr, ',');
-      LOG(info) << Form("%s%d", "Fixing chamber: ", std::stoi(substr));
-      mAlign.FixChamber(std::stoi(substr));
+    TString chambersString = ic.options().get<string>("fix-chamber");
+    std::unique_ptr<TObjArray> objArray(chambersString.Tokenize(","));
+    if (objArray->GetEntries() > 0) {
+      for (int iVar = 0; iVar < objArray->GetEntries(); ++iVar) {
+        LOG(info) << Form("%s%d", "Fixing chamber: ", std::stoi(objArray->At(iVar)->GetName()));
+        mAlign.FixChamber(std::stoi(objArray->At(iVar)->GetName()));
+      }
+    }
+
+    // Fix DEs
+    TString DEString = ic.options().get<string>("fix-de");
+    TString MaskDEString = ic.options().get<string>("mask-fix-de");
+    std::unique_ptr<TObjArray> objArrayDE(DEString.Tokenize(","));
+    std::unique_ptr<TObjArray> objArrayMask(MaskDEString.Tokenize(","));
+    if (objArrayDE->GetEntries() > 0) {
+      if (objArrayDE->GetEntries() != objArrayMask->GetEntries()) {
+        LOG(fatal) << "Inconsistent size of DEs and Masks!";
+      }
+      for (int iVar = 0; iVar < objArrayDE->GetEntries(); ++iVar) {
+        LOG(info) << Form("%s%d%s%d", "Fixing DE: ", std::stoi(objArrayDE->At(iVar)->GetName()), " with mask: ", std::stoi(objArrayMask->At(iVar)->GetName()));
+        mAlign.FixDetElem(std::stoi(objArrayDE->At(iVar)->GetName()), std::stoi(objArrayMask->At(iVar)->GetName()));
+      }
     }
 
     doMatched = ic.options().get<bool>("matched");
@@ -902,6 +926,14 @@ o2::framework::DataProcessorSpec getAlignmentSpec(bool disableCCDB)
             {"matched", VariantType::Bool, false, {"Switch for using MCH-MID matched tracks"}},
             {"fix-chamber", VariantType::String, "", {"Chamber fixing, ex 1,2,3"}},
             {"use-record", VariantType::Bool, false, {"Option for directly using record in alignment if provided"}},
+            {"variation-x", VariantType::Float, 2.0, {"Allowed variation for x axis in cm"}},
+            {"variation-y", VariantType::Float, 0.3, {"Allowed variation for y axis in cm"}},
+            {"variation-phi", VariantType::Float, 0.002, {"Allowed variation for phi axis in rad"}},
+            {"variation-z", VariantType::Float, 2.0, {"Allowed variation for z axis in cm"}},
+            {"sigma-x", VariantType::Float, 1000.0, {"Sigma cut along X"}},
+            {"sigma-y", VariantType::Float, 1000.0, {"Sigma cut along Y"}},
+            {"fix-de", VariantType::String, "", {"DE fixing, ex 101,1019"}},
+            {"mask-fix-de", VariantType::String, "", {"Mask for DE d.o.f fixing, ex 0,2,4"}},
             {"output", VariantType::String, "Alignment", {"Option for name of output file"}}}};
 }