This page does a good job of explaining the complexity of why the way the Slicer works the way it works, but does not necessarily help them very much. Here is what I get following the suggestion of resampling via CropVolume:
This is confusing because, the only way I can see my newly resampled volume in the rotated orientation is when I choose the “reformat” axis. If I click on the sagittal, it goes back to the untransformed orientation. What I am going to do when I wanted to see the new volume what I think is the axial plane? Click axial, and expand the dialog box and click rotate volume to plane? This is too much in my opinion. Not only this is still confusing, it doesn’t resolve the issue of exported volume will still not be read in the anticipated direction in ImageJ or others, even though the user thinks they resampled the volume (It just looks like noisy volume).
I understand why you guys are doing this, Slicer is a predominantly for medical imaging, and you don’t want to mess with the acquired data randomly. But that’s not common for our datasets (again it is very common for scans to be in totally random orientation). So what we need is a tool (as part of SlicerMorph, not in core Slicer) to resample the volume with the warning to the user that this will potentially degrade their volume, particularly if they keep doing it (transform ->resample, then further transform and resample). But it is a need.