ENH: Prepare for merge with svn master.

ANTS.cmake

@@ -6,6 +6,7 @@ cmake_minimum_required(VERSION 2.8.2)
 set(ANTS_TEST_BIN_DIR ${CMAKE_BINARY_DIR}/Examples)
 
 add_subdirectory(Examples)
+
 ###
 #  Perform testing
 ###

Examples/CMakeLists.txt

@@ -339,6 +339,7 @@ set(DATA_DIR ${CMAKE_CURRENT_LIST_DIR}/Data)
 set(R16_IMAGE ${DATA_DIR}/r16slice.nii.gz)
 set(R64_IMAGE ${DATA_DIR}/r64slice.nii.gz)
 
+if (0) ## This test is not yet completed.
 add_test(antsRegistrationTest1 ${TEST_BINARY_DIR}/antsRegistration -d 2
   -m mi[  ${R16_IMAGE}, ${R64_IMAGE} , 1 , 20, Regular , 0.05 ]
   -t affine[ 1.0 ]
@@ -352,6 +353,7 @@ add_test(antsRegistrationTest1 ${TEST_BINARY_DIR}/antsRegistration -d 2
   -f 3x2x1
   -u 1
   -o [xtest_CC,xtest_CC.nii.gz,xtest_CC_inv.nii.gz] )
+endif()
 
 
 #set(CurrentExe "GlamorousGlue")

Utilities/antsSCCANObject.hxx

@@ -2035,10 +2035,18 @@ TRealType antsSCCANObject<TInputImage, TRealType>
     std::cout << " You need to define a reference matrix " << std::endl;
     exit(1);
     }
-  this->m_VariatesP.set_size( this->m_MatrixP.cols(), n_vecs  );
-  this->m_VariatesP.fill(0);
-  VectorType intercept( this->m_MatrixP.cols(), 1);
-  this->m_VariatesP.set_column( 0, intercept );
+  MatrixType A;
+  MatrixType rmat = this->m_OriginalMatrixR.extract(
+      this->m_OriginalMatrixR.rows(), this->m_OriginalMatrixR.cols() - 1, 0, 1 );
+  rmat = this->NormalizeMatrix( rmat );
+  unsigned int extra_cols = 0;
+  this->m_VariatesP.set_size( this->m_MatrixP.cols(), n_vecs + extra_cols );
+  this->m_VariatesP.fill( 0 );
+  VectorType intercept( this->m_MatrixP.cols(), 1 );
+  if( extra_cols > 0 )
+    {
+    this->m_VariatesP.set_column( 0, intercept );
+    }
   RealType   lmerror = 0.0;
   VectorType original_b =  this->m_MatrixR.get_column( 0 );
   for(  unsigned int colind = extra_cols; colind < this->m_VariatesP.cols(); colind++ )