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GCPs with Ellipsoid heights - better to convert to Orthometric prior to processing?

I have a project where I collected GCPs but I noticed that the elevation values were recorded in ellipsoid height rather than orthometric (relative to MSL), the latter being what I am aiming for. 

Is it a best practice to convert the Z values to orthometric prior to processing to ensure my final terrain data reads relative to MSL, or will it be automatic as long as a choose MSL (egm96) from vertical output option?

Thank you

… the horizontal coordinate system set to record was NAD83 UTM Zone 9N and I was expecting orthometric Z values but they seem to be ellipsoid heights.

Update: I have now marked some of the GCPs in the RayCloud and noticing that the Z values are being computed 20+ metres difference.  To me this is a good sign, as it seems to be shifting the Z relative to MSL.  The other shift on X and Y seem to minimal which is what I expected.

The Z shift is stated as an “error” from initial position… but is this just attributed to the orthometric shift based on the fact that I’m asking Pix4D to export MSL values?  In other words, is this normal or should I be fixing something with my GCP inputs.  Thanks



Hello Mike,

What is important is that the selected coordinate system (horizontal and vertical) for the GCPs reflects the imported values. That means that if the GCPs are referenced to the ellipsoid you should select the ellipsoid option (Geoid Height Above Ellipsoid 0), while if the GCPs heights are converted to orthometric heights, one of the geoid models should be selected in the Vertical Coordinate System section. 

To which surface the GCPs are referenced? Did you import the ellipsoid or orthometric heights? The difference between the initial and computed Z should not be so large.
Could you please attach here the quality report of the project so that I better understand the problem?