Hi, I am looking at the nrrd file downloadable from the ReferenceSpaceCache, querying for the 100um template stack. If I look in the header, I get the following space description:
('space', 'left-posterior-superior'), ('sizes', array([132, 80, 114]))
space entry does not match, as the stack axes order should be PIR (but see later) as specified in the documentation.
Second problem. I am confused by the fact that reading here one would assume that origin (voxel [0, 0, 0]) of the stack template stack numpy array should be anterior, superior, left; but the stack that I get with ReferenceSpaceCache has voxel [0, 0, 0] in the anterior, superior, right corner. Has this to do with the confusion between image/numpy ij indexing vs cartesian coordinate system?