Docs / PatientSliceOrientation
We must point out that (X)MedCon is entirely ignorant to orientation. The orientation of patient and slices is a very complicated issue. Besides, not all formats support a proper notation. And if information is available, it's still tricky, incomplete or misused. The simple policy is:
(X)MedCon does not handle, neither change orientations
(X)MedCon merely copies (preserves) the header information and reads, writes or views the raw image arrays as they are stored in the originating file: from top to bottom, from left to right, and this slice by slice. Maybe (X)MedCon misses or wrongfully interprets the fields concerning the orientation, but we are confident that the image arrays will be saved according to the original file. The rare cases in which (X)MedCon changes orientation are purely user specific choices, like reverse sort of all slices, flipping images or an explicit reslicing.
Because (X)MedCon does need a way of preserving or filling in missing orientation information, while being suitable for all formats, we choose for the most complete (complex) definition used in the DICOM 3.0 standard. The standard is based on (a) right-handed coordinate system, (b) the 3D coordinate values of the origin of the image and (c) the directions of two unit vectors in this origin. What follows is an explanation of what the DICOM 3.0 notation holds.