[ITK] [ITK-users] ExtractSliceImageFilter & image orientation

[Matt McCormick]

Hello Christina,


One option may be to call SetDirectionCollapseToStrategy on
ExtractImageFilter:


https://itk.org/Doxygen/html/classitk_1_1ExtractImageFilter.html#a5b3bcfa552d8ad7cf509e32209aadc13

This approach addresses the Image Direction matrix.


Another option is to use FlipImageFilter:

  https://itk.org/Doxygen/html/classitk_1_1FlipImageFilter.html

instead of OrientImageFilter.


Hope this helps,
Matt

On Fri, Mar 3, 2017 at 10:32 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> Hi,
>
> I'd like to extract a sagittal slice from a 3d image volume. The
> application should be quite flexible and thus be able to process axial,
> coronal and sagittal image volumes.
>
> This is my mini pipeline: OrientImageFilter -> ExtractImageFilter
>
> The problem is that I keep getting the slice rotated 90° and flipped. ITK
> snap renderes the volume correctly with correct orientation labels. I've
> attached the source code and the input data volume. Of course I could
> rotate and flip the slice back, but that's not very elegant...
>
> Any hints what is going wrong here?
>
> Regards,
>
> Christina Roßmanith
>
>
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