From ca615ab9784d7402c4d0001985843af8c5761c39 Mon Sep 17 00:00:00 2001
From: Dzenan Zukic <dzenan.zukic@kitware.com>
Date: Wed, 29 Aug 2018 15:28:15 -0400
Subject: [PATCH 1/2] Updating ITK to latest 4.13 release branch and updating
 BRAINSTools

This is the last version of BRAINSTools before it started
requiring CMake version higher than 3.5.0

Legacy code is disabled for ITK, in preparation for switch to version 5.0.
---
 Libs/MRML/Core/vtkITKTransformConverter.h | 4 ----
 SuperBuild.cmake                          | 2 +-
 SuperBuild/External_ITKv4.cmake           | 4 ++--
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/Libs/MRML/Core/vtkITKTransformConverter.h b/Libs/MRML/Core/vtkITKTransformConverter.h
index 814765935..91de540bc 100644
--- a/Libs/MRML/Core/vtkITKTransformConverter.h
+++ b/Libs/MRML/Core/vtkITKTransformConverter.h
@@ -579,11 +579,7 @@ template <typename BSplineTransformType> bool vtkITKTransformConverter::SetITKBS
   // * mesh origin X, Y, Z (position of the boundary node before the grid)
   // * mesh spacing X, Y, Z
   // * mesh direction 3x3 matrix (first row, second row, third row)
-#if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1
   typename BSplineTransformType::FixedParametersType transformFixedParamsItk;
-#else                                         //Pre 4.8.1
-  typename BSplineTransformType::ParametersType transformFixedParamsItk;
-#endif
   const unsigned int numberOfFixedParameters=VTKDimension*(VTKDimension+3);
   transformFixedParamsItk.SetSize(numberOfFixedParameters);
 
diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index af89cc7f7..c070426c7 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -259,7 +259,7 @@ set(BRAINSTools_options
   )
 Slicer_Remote_Add(BRAINSTools
   GIT_REPOSITORY "${EP_GIT_PROTOCOL}://github.com/Slicer/BRAINSTools.git"
-  GIT_TAG "c60de5558a5fcb731ef30c1acef478b76bd036fd" # master (from 2017-11-29, post v4.7.1)
+  GIT_TAG "87da22c2e365da72d3c0dea2634c4efa73dbeab3" # 2017-12-09
   LICENSE_FILES "http://www.apache.org/licenses/LICENSE-2.0.txt"
   OPTION_NAME Slicer_BUILD_BRAINSTOOLS
   OPTION_DEPENDS "Slicer_BUILD_CLI_SUPPORT;Slicer_BUILD_CLI"
diff --git a/SuperBuild/External_ITKv4.cmake b/SuperBuild/External_ITKv4.cmake
index c5c0ce52c..231c1bf88 100644
--- a/SuperBuild/External_ITKv4.cmake
+++ b/SuperBuild/External_ITKv4.cmake
@@ -33,7 +33,7 @@ if(NOT DEFINED ITK_DIR AND NOT Slicer_USE_SYSTEM_${proj})
 
   ExternalProject_SetIfNotDefined(
     Slicer_${proj}_GIT_TAG
-    "bc0d1723cb4442be2f74ae4585d6c6be1029e3a4" # slicer-v4.13.0-2018-05-25-32608b68bd
+    "a44f430b3edb5fff62671b4ba87cf41c60ee272b" # slicer-v4.13.1-2018-08-17-cdc3e57
 
     QUIET
     )
@@ -98,7 +98,7 @@ if(NOT DEFINED ITK_DIR AND NOT Slicer_USE_SYSTEM_${proj})
       -DITK_INSTALL_LIBRARY_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
       -DBUILD_TESTING:BOOL=OFF
       -DBUILD_EXAMPLES:BOOL=OFF
-      -DITK_LEGACY_REMOVE:BOOL=OFF
+      -DITK_LEGACY_REMOVE:BOOL=ON
       -DITKV3_COMPATIBILITY:BOOL=OFF
       -DITK_BUILD_DEFAULT_MODULES:BOOL=ON
       -DModule_ITKReview:BOOL=ON
-- 
GitLab


From 32c3b64889c54f165fa7a17847b9a2d8972b1206 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= <dzenan.zukic@kitware.com>
Date: Mon, 3 Sep 2018 09:55:10 -0400
Subject: [PATCH 2/2] COMP: SetProcessDPIAware() needs WinUser.h for building
 on Windows

---
 Base/QTApp/qSlicerApplicationHelper.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Base/QTApp/qSlicerApplicationHelper.cxx b/Base/QTApp/qSlicerApplicationHelper.cxx
index 1f25fbc6f..e332144a5 100644
--- a/Base/QTApp/qSlicerApplicationHelper.cxx
+++ b/Base/QTApp/qSlicerApplicationHelper.cxx
@@ -66,6 +66,10 @@
 # include <PythonQtPythonInclude.h>
 #endif
 
+#ifdef _WIN32
+#include <Windows.h> //for SetProcessDPIAware
+#endif
+
 //----------------------------------------------------------------------------
 qSlicerApplicationHelper::qSlicerApplicationHelper(QObject * parent) : Superclass(parent)
 {
-- 
GitLab