Thanks! @pieper
The z positions of the raw images (raw_corners) & the ones I set up manually in my script are quite different from the ones I got from both originalCorners and targetCorners before and after grid transforms.
In the raw slices, there are large gaps between slices 5 and 6, slices 105 and 106, and slices 205 and 206 (-61, -116 and -116 respectively). When it was loaded, the z spacing between adjacent slices was all updated to 0.58:
This is indeed a very weird dataset. I felt like the scans were acquired 3 separate times and concatenated together. I suspected the slice below might show the poor concatenation
