I have the following problem when transforming Nifti files. Because they are not transfomed correctly. My procedure is the following:
I open the nifti file.
I go to the Transform tab , create a new linear transform and then under apply transform move the nifti from Transformable to Transform. Only then I can see what changes when I turn the rotation sliders.
when I have set everything so far, I go back to Data. 4.
then I click on the nifti and make harden Transform.
when I save now, it saves but when I reload it, it looks like the transform was done twice.
I have the same thing when i click on the eye once to hide it and then click on it again to show it.
Maybe someone here can help me or knows a similar problem, thanks a lot
Check that you are configured to see the patient view rather than the image-referenced view, which you can set as described in the link below. Note you can also volume render or make the slice views visible in 3D to see the effect of the transforms.
As a side note, nii files are slightly lossy because they store the transform with 32bit floats while Slicer internally uses 64bit which is better preserved in formats like nrrd and dicom. This may sound like a small detail but it can lead to visibly different results or numerical errors when comparing orientations.