Hi Andras,
Thanks for the help!
Unfortunately, I have tried hardening the transforms to no avail.
I’ve also looked for the “Apply Transforms” option in “Export to file…” and the “Apply Transforms” option doesn’t seem to be present for any of the available export file formats. I went down the list selecting all of them and looking for an “Apply Transforms” option and none appeared. The only export option seemed to be “Compress” (see example screenshot below).
Can I simply create an empty volume via an axis-aligned region of interest? Presumably that would have a transform basically equivalent to the identity matrix, and then if I resample data via “Registration → Resample Image (BRAINS)” using that empty volume as the “Reference Image” I should end up with voxel data that’s all axis aligned and doesn’t then require any external software to understand any transform that needs to be applied to the data?
The only result I can find from a Google search regarding creation of an empty volume is this (using the “Image Maker” CLI extension):
https://slicer.readthedocs.io/en/latest/developer_guide/script_repository/volumes.html
… which I’d rather not do because I’m trying to keep this GUI based for future reference by other users.
There’s also this post from yourself back in 2018:
… but I’m not sure if that’s still valid. You did mention “We’ll figure out some way to not require this step (maybe create a blank volume), but right now you need to do this” and it seems you still need to do this five years later?
Do I have to create a suitable empty volume data set in e.g. FIJI and then load it into Slicer?