I’m re-posting a question that I recently asked in the SimpleITK Discourse (https://discourse.itk.org/t/direction-orientation-matrix-dicom-vs-nifti/3289). It may seem a bit redundant, but I would like to have your thoughts considering that conversion DICOM to Nifti is the initial step in the creation of a BIDS structure.
In short, using ITK based tools (elastix, ANTS, SimpleITK, MeVisLab, and maybe more), I notice that the Direction Matrix I read from DICOMs is different compared to the one is set in Niftis for the same image. This affects some algorithms working in world coordinates, particularly registration operations.
Have any of you perceived these inconsistencies with the Niftis ? There is a good amount of info on the q_form and s_form of the orientation matrix in Niftis, but I have not seen any formal consistency checks between the original DICOMs and generated Niftis. Are you aware of anything like this?