[Vv] Bug in clitkCropImage with the --like option

[Benoît Presles]

Dear Thomas,

A quick email just to inform you that there is a bug in the 
clitkCropImage tool with the --like option. Indeed, the output image has 
always an identity direction cosines matrix even if the like image does 
not have an identity direction cosines matrix.

To correct the bug, I updated the itk/clitkCropLikeImageFilter.txx file 
as follows:

@@ -101,14 +101,19 @@ GenerateOutputInformation() {
    // Get input info
    typename ImageType::SizeType likeSize;
    typename ImageType::IndexType likeStart;
-  typename ImageType::PointType likeOrigin;
-  typename ImageType::SpacingType likeSpacing;
-  if (m_LikeImage) {
+  typename ImageType::PointType likeOrigin;
+  typename ImageType::SpacingType likeSpacing;
+  typename ImageType::DirectionType likeDirection;
+  typename ImageType::DirectionType like_invDirection;
+  if (m_LikeImage) {
      likeSize = m_LikeImage->GetLargestPossibleRegion().GetSize();
      likeStart = m_LikeImage->GetLargestPossibleRegion().GetIndex();
      likeOrigin = m_LikeImage->GetOrigin();
      likeSpacing = m_LikeImage->GetSpacing();
-    output->CopyInformation(m_LikeImage);
+    likeDirection = m_LikeImage->GetDirection();
+    //I don't know really why I need the inverse...
+    like_invDirection = likeDirection.GetInverse();
+    //output->CopyInformation(m_LikeImage);
    }
    else {
      // Only load the header (allows to use 'like' with any image type)
@@ -119,7 +124,11 @@ GenerateOutputInformation() {
          likeStart[i] = 0;//header->GetIORegion().GetIndex()[i];
          likeOrigin[i] = header->GetOrigin(i);
          likeSpacing[i] = header->GetSpacing(i);
+        for(unsigned int j=0; j<ImageType::ImageDimension; j++)
+            likeDirection[i][j] = header->GetDirection(i)[j];
        }
+      //I don't know really why I need the inverse...
+      like_invDirection = likeDirection.GetInverse();
      }
      else {
        clitkExceptionMacro("You should provide SetCropLikeFilename or 
SetCropLike to CropLikeImageFilter");
@@ -150,8 +159,9 @@ GenerateOutputInformation() {
    output->SetRegions(m_OutputRegion);
    output->SetRequestedRegion(m_OutputRegion);
    output->SetBufferedRegion(m_OutputRegion);
-  output->SetSpacing(likeSpacing);
+  output->SetSpacing(likeSpacing);
    output->SetOrigin(likeOrigin);
+  output->SetDirection(like_invDirection);
    output->Allocate(); // Needed ?

    // get startpoint source/dest



Best regards,
Ben