After looking at this in more detail, I’m not convinced that the new GDCM behavior about using the SpacingBetweenSlices is actually incorrect. I’ll comment on why in the ITK issue.
For Slicer, the issue has something to do with how non-right-handed direction matrices are handled. If I add this line
seriesReader->SetForceOrthogonalDirection(false);
in vtkITKArchetypeImageSeriesReader::RequestInformation then the volume loads correctly. Without it the image loads upside down and the acquisition transform is not able to fix it.
But since that option about orthogonal directions has been around for six years it seems that something else recently has broken the path when this flag is not set, and perhaps that is due to the negative spacing.
I’m not sure when I’ll have a chance to dig into this more so I thought I’d post this note in case @lassoan, @jcfr, @issakomi, or others know more.