[ITK] change orientation of images with OrientImageFilter

[Butlers Home]

On 29 July 2014 18:27, Andras Lasso <lasso at queensu.ca> wrote:

>  As it is described at http://www.na-mic.org/Bug/view.php?id=2173: update
> of the image pose is implemented in ITK for some formats (for example for
> NRRD it is implemented in itkNrrdImageIO.cxx), while it is not implemented
> for MetaIO (probably it should have been implemented in itkMetaImageIO.cxx).
>

I see that this will not change in the near future since the bug was
submitted 2 years ago. I will try to find a workaround and post updates in
case it works.


>
>
> Andras
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>
> *From:* Community [mailto:community-bounces at itk.org] *On Behalf Of *Butlers
> Home
> *Sent:* Tuesday, July 29, 2014 12:03 PM
> *Cc:* community at itk.org
> *Subject:* Re: [ITK] change orientation of images with OrientImageFilter
>
>
>
>
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> On 29 July 2014 17:22, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>
>  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.
>
>
>
> The matrices stay the same: For example
>
> [-0.5    0    0    0
>
>  0     -0.5   0    0
>
>  0        0   0.5  1]        is the same for LSP and RAI orientations.
>
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>
> 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've also checked their positions with Slicer and it yields the same
> interpretation. However, if what you say is true, then any visualizer
> should yield the same output provided that the same physical location is
> preserved. I still don't understand why one would not display the image
> with the orientation that corresponds to its specifications.
>
>
>
>
>
> 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");
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>
>
> imReader1->Update();
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>
>
> // 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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>
>
>
>
>  Best,
>
> --
>
> Butlers
>

Thank you everyone for your suggestions and clarifications.


-- 
Butlers
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