Operating system: Windows 10
Slicer version: 4.6.2
Expected behaviour: After hardening transform, saved image volume will preserve transformed state when opened outside Slicer
Actual behaviour: Image returns to original (un-transformed) orientation when opened outside Slicer
I am trying to perform a simple rotation transformation to a .mha volume and then save the transformed result to be available outside of Slicer; however, when I open the saved result outside of Slicer, the image returns to its original orientation.
I have hardened the transform before saving and I have also tried using “Resample Scalar Volume” on the transformed image but it both cases the image returns to its original orientation when opened in a variety of programs (ex. VolView, MATLAB,…) outside of Slicer. It should be noted that when the saved volumes are re-opened in Slicer, the transform is applied. Additionally, the transform does appear in the .mha TransformMatrix header field.
I also tried exporting the transformed/resampled images as DICOM series, in case it was an incompatibility with the .mha format but this had the same un-transformed result outside of Slicer. I also tried all options with the “Ignore Orientation” option selected and deselected on data import (suggestion found from a similar question from 2012 online: http://slicer-users.65878.n3.nabble.com/Non-warping-fiducial-transform-not-present-in-saved-volume-td4025526.html).
I appreciate any help you can offer and thank you!
Summary of approaches tried:
Hardening transform and saving as .mha and DICOM
Resampling transformed image and saving as .mha and DICOM
Import data with/without “Ignore Orientation” option selected and repeating 2 items above