Transformation output files

[mikebind (Mike Bindschadler)]

Slicer uses an RAS coordinate system internally, whereas ITK (and much of the rest of the medical imaging world) has settled on using an LPS coordinate system. Respecting this, exports from Slicer are automatically converted to use LPS, and imports from LPS are handled correctly. However, when you compare the internal representation of a transformation in Slicer with the same transformation in some other program they will not match because of the change in coordinate system.

I know I’ve seen this come up many times in the forum, so if you are looking for more information, keep searching here. Here is one related post I found:

Npy transform matrix

Slicer uses all data in LPS coordinate system in files (following conventions set by DICOM, ITK, and most other modern medical image computing software), while uses RAS in the scene (for backward compatibility). You need to apply LPS<->RAS basis transform if you import an LPS transform as shown here. You also need to be aware of the transform direction (modeling/resampling; from/to parent).