GCP's and images in different height system

Hi
I have set of images taken with DJI Mavic 3M drone, it has RTK, so I have coordinates in WGS and ellipsoidal height. I also have 10 GCP’s for georeferencing, but it is in epsg 3346 (LKS-94) coordinate system, and LAS07 height systems (Lithuanian), coordinates is translating correctly, but height difference is around 23 meters. Once I align images without control points, all images joins into one component. Once I import GCP coordinates and link it to corresponding images it shows that error is around 23 meters, so I assume it is due to difference in height. Once I align it again, with control points attached, I get misalignment (some images is at LAS07 height, some at ellipsoidal height.




I am attaching few images. I have set my project and output coordinate system to epsg 3346 (LKS-94).

Hello Martynas,
the best thing there will be turn off the camera priors and use only the GCPs for georeferencing.
Then you will get the model in a wanted coordinate systems.
The height difference could be caused by the difference between ellipsoidal and geoid heights.

Hi Ondrej,
Does that mean set images Absolute pose to unknown?

Yes, I meant that.