[ITK] change orientation of images with OrientImageFilter

[Bradley Lowekamp]

Hello Butlers,

Just because the images look the same doesn't mean the filter didn't have an effect! Does ITK-SNAP have a way to look at the orientation of the direction cosine matrix? This should be different between the two images.

My understanding of that orientation filter was that it changed the direction cosines AND the order of the pixels such that they still have the same physical location. Since you are using a viewer which is aware of this information I would not expect the image to visually change.

I don't know how that orientation field in the MHA file is used... others have already chimed in on that.

Brad

On Jul 29, 2014, at 10:13 AM, Butlers Home <butlershomecoffee at gmail.com> wrote:

> I would like to know how I can change the orientation of two 3D images.
> Scenario:
> - both images are .mha
> - one image has RAI as the initial orientation
> - 2nd image has LPS as the initial orientation
> 
> I would like to set the same orientation RAI for both images before processing them (i.e., registering them in my case). With the below mentioned code I manage to change the orientation specified textually in the .mha files but visually they do not change. Why is that? Is the orientation changing just within the header specifications without actually changing the visualization part? For visualization I used ITK-SNAP.
> 
> Here is a code snippet from what I do:
> 
> [...]
> 
> typedef itk::ImageFileReader< ImageType2 > ImageReaderType1;
> typedef itk::ImageFileReader< ImageType1 > ImageReaderType2;
> 
> ImageReaderType1::Pointer imReader1 = ImageReaderType1::New();
> ImageReaderType2::Pointer imReader2 = ImageReaderType2::New();
> 
> imReader1->SetFileName("im1.mha");
> imReader2->SetFileName("im2.mha");
> 
> imReader1->Update();
> 
> // set both images to same orientation
> 
> // orientation filter for 1st image
> itk::OrientImageFilter<ImageType1, ImageType1>::Pointer orienter1 = itk::OrientImageFilter<ImageType1, ImageType1>::New();
> orienter1->UseImageDirectionOn();
> orienter1->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);
> orienter1->SetInput(imReader1->GetOutput());
> orienter1->Update();
> 
> // orientation filter for 2nd image
> itk::OrientImageFilter<ImageType2, ImageType2>::Pointer orienter2 = itk::OrientImageFilter<ImageType2, ImageType2>::New();
> orienter2->UseImageDirectionOn();
> orienter2->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);
> orienter2->SetInput(imReader2->GetOutput());
> orienter2->Update();
> 
> [...]
> 
> I tried not using the cosine-based approach, i.e., use the itk::AnalyzeImageIO class together with itk::ExposeMetaData<>() but for some unknown reason, the orientation is not determined appropriately. I would also prefer not using them at all because, as far as I understood, they are deprecated.
> 
> Thank you.
> 
> Best regards,
> --
> Butlers
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