diff --git a/AutoWorkup/BAWantsRegistrationBuildTemplate.py b/AutoWorkup/BAWantsRegistrationBuildTemplate.py
index 3d240688..0ec3eb0b 100644
--- a/AutoWorkup/BAWantsRegistrationBuildTemplate.py
+++ b/AutoWorkup/BAWantsRegistrationBuildTemplate.py
@@ -198,22 +198,24 @@ def BAWantsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
     BeginANTS.inputs.dimension = 3
     """ This is the recommended set of parameters from the ANTS developers """
     BeginANTS.inputs.output_transform_prefix = str(iterationPhasePrefix) + '_tfm'
-    BeginANTS.inputs.transforms = ["Rigid", "Affine", "SyN"]
-    BeginANTS.inputs.transform_parameters = [[0.1], [0.1], [0.15, 3.0, 0.0]]
-    BeginANTS.inputs.metric = ['Mattes', 'Mattes', 'CC']
-    BeginANTS.inputs.sampling_strategy = ['Regular', 'Regular', None]
-    BeginANTS.inputs.sampling_percentage = [0.1, 0.1, 1.0]
-    BeginANTS.inputs.metric_weight = [1.0, 1.0, 1.0]
-    BeginANTS.inputs.radius_or_number_of_bins = [32, 32, 4]
-    BeginANTS.inputs.number_of_iterations = [[2000, 2000, 2000], [1000, 1000, 1000], [10000, 500, 500, 200]]
-    BeginANTS.inputs.convergence_threshold = [5e-7, 5e-7, 5e-7]
-    BeginANTS.inputs.convergence_window_size = [15, 15, 15]
-    BeginANTS.inputs.use_histogram_matching = [True, True, True]
-    BeginANTS.inputs.shrink_factors = [[4, 2, 1], [4, 2, 1], [6, 4, 2, 1]]
-    BeginANTS.inputs.smoothing_sigmas = [[4, 2, 0], [4, 2, 0], [6, 4, 2, 0]]
-    BeginANTS.inputs.use_estimate_learning_rate_once = [False, False, False]
+    BeginANTS.inputs.transforms = ["Rigid", "Similarity", "Affine", "SyN"]
+    BeginANTS.inputs.transform_parameters = [[0.1], [0.1], [0.1], [0.15, 3.0, 0.0]]
+    BeginANTS.inputs.metric = ['Mattes', 'Mattes', 'Mattes', 'CC']
+    BeginANTS.inputs.sampling_strategy = ['Regular', 'Regular', 'Regular', None]
+    BeginANTS.inputs.sampling_percentage = [1.0, 1.0, 1.0, 1.0]
+    BeginANTS.inputs.metric_weight = [1.0, 1.0, 1.0, 1.0]
+    BeginANTS.inputs.radius_or_number_of_bins = [32, 32, 32, 4]
+    BeginANTS.inputs.convergence_threshold = [5e-7, 5e-7, 5e-7, 5e-7]
+    BeginANTS.inputs.convergence_window_size = [25, 25, 25, 25]
+    BeginANTS.inputs.use_histogram_matching = [True, True, True, True]
+    BeginANTS.inputs.number_of_iterations = [[2000, 2000], [2000, 2000], [1000, 1000, 100], [10000, 500, 500, 200]]
+    BeginANTS.inputs.smoothing_sigmas = [[4, 2], [5, 2], [4, 2, 1], [5, 4, 2, 0]]
+    BeginANTS.inputs.shrink_factors = [[4, 2], [5, 2], [4, 2, 1], [5, 4, 2, 1]]
+    BeginANTS.inputs.use_estimate_learning_rate_once = [False, False, False, False]
     BeginANTS.inputs.write_composite_transform = True
     BeginANTS.inputs.collapse_output_transforms = True
+    BeginANTS.inputs.winsorize_lower_quantile = 0.025
+    BeginANTS.inputs.winsorize_upper_quantile = 0.975
     BeginANTS.inputs.output_warped_image = 'atlas2subject.nii.gz'
     BeginANTS.inputs.output_inverse_warped_image = 'subject2atlas.nii.gz'
 
diff --git a/AutoWorkup/WorkupT1T2.py b/AutoWorkup/WorkupT1T2.py
index 776ef9cf..91d954a2 100644
--- a/AutoWorkup/WorkupT1T2.py
+++ b/AutoWorkup/WorkupT1T2.py
@@ -693,15 +693,15 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
                     AtlasToSubjectantsRegistration[sessionid].inputs.transform_parameters = [[0.1], [0.15, 3.0, 0.0]]
                     AtlasToSubjectantsRegistration[sessionid].inputs.metric = ['Mattes', 'CC']
                     AtlasToSubjectantsRegistration[sessionid].inputs.sampling_strategy = ['Regular', None]
-                    AtlasToSubjectantsRegistration[sessionid].inputs.sampling_percentage = [0.1, 1.0]
+                    AtlasToSubjectantsRegistration[sessionid].inputs.sampling_percentage = [1.0, 1.0]
                     AtlasToSubjectantsRegistration[sessionid].inputs.metric_weight = [1.0, 1.0]
                     AtlasToSubjectantsRegistration[sessionid].inputs.radius_or_number_of_bins = [32, 4]
                     AtlasToSubjectantsRegistration[sessionid].inputs.number_of_iterations = [[1000, 1000, 1000], [10000, 500, 500, 200]]
                     AtlasToSubjectantsRegistration[sessionid].inputs.convergence_threshold = [5e-7, 5e-7]
-                    AtlasToSubjectantsRegistration[sessionid].inputs.convergence_window_size = [15, 15]
+                    AtlasToSubjectantsRegistration[sessionid].inputs.convergence_window_size = [25, 25]
                     AtlasToSubjectantsRegistration[sessionid].inputs.use_histogram_matching = [True, True]
-                    AtlasToSubjectantsRegistration[sessionid].inputs.shrink_factors = [[4, 2, 1], [6, 4, 2, 1]]
-                    AtlasToSubjectantsRegistration[sessionid].inputs.smoothing_sigmas = [[4, 2, 0], [6, 4, 2, 0]]
+                    AtlasToSubjectantsRegistration[sessionid].inputs.shrink_factors = [[4, 2, 1], [5, 4, 2, 1]]
+                    AtlasToSubjectantsRegistration[sessionid].inputs.smoothing_sigmas = [[4, 2, 0], [5, 4, 2, 0]]
                     AtlasToSubjectantsRegistration[sessionid].inputs.use_estimate_learning_rate_once = [False, False]
                     AtlasToSubjectantsRegistration[sessionid].inputs.write_composite_transform = True
                     AtlasToSubjectantsRegistration[sessionid].inputs.collapse_output_transforms = True
diff --git a/BRAINSCommonLib/BRAINSFitSyN.h b/BRAINSCommonLib/BRAINSFitSyN.h
index ea79b2e3..40045577 100644
--- a/BRAINSCommonLib/BRAINSFitSyN.h
+++ b/BRAINSCommonLib/BRAINSFitSyN.h
@@ -17,8 +17,8 @@ simpleSynReg( typename FixedImageType::Pointer & infixedImage,
 
   typename SyNRegistrationHelperType::Pointer regHelper = SyNRegistrationHelperType::New();
     {
-    const float lowerQuantile = 0.0;
-    const float upperQuantile = 1.0;
+    const float lowerQuantile = 0.025;
+    const float upperQuantile = 0.975;
     const bool  doWinsorize(false);
     regHelper->SetWinsorizeImageIntensities(doWinsorize, lowerQuantile, upperQuantile);
     }
@@ -48,7 +48,7 @@ simpleSynReg( typename FixedImageType::Pointer & infixedImage,
     }
     {
     std::vector<unsigned int> convergenceWindowSizeList;
-    const unsigned int        convergenceWindowSize = 15;
+    const unsigned int        convergenceWindowSize = 25;
     convergenceWindowSizeList.push_back(convergenceWindowSize);
     regHelper->SetConvergenceWindowSizes( convergenceWindowSizeList );
     }
@@ -57,7 +57,7 @@ simpleSynReg( typename FixedImageType::Pointer & infixedImage,
     // --shrink-factors 3x2x1
     std::vector<std::vector<unsigned int> > shrinkFactorsList;
     std::vector<unsigned int>               factors(4);
-    factors[0] = 6;
+    factors[0] = 5;
     factors[1] = 4;
     factors[2] = 2;
     factors[3] = 1;
@@ -68,7 +68,7 @@ simpleSynReg( typename FixedImageType::Pointer & infixedImage,
     // --smoothing-sigmas 3x2x0
     std::vector<std::vector<float> > smoothingSigmasList;
     std::vector<float>               sigmas(4);
-    sigmas[0] = 6;
+    sigmas[0] = 5;
     sigmas[1] = 4;
     sigmas[2] = 2;
     sigmas[3] = 0;