I have a phantom 4 RTK drone that captures all of its data in WGS84. In order to compare my data with Civil Engineering surveys of the same area I need to convert the vertical coordinate data into NAVD88. Is there a way this can be done in Pix4D? If so, would someone please describe the workflow and settings, specifically the output coordinate settings that must be selected in relation to the vertical datum?
For the vertical coordinate system, the following options are available in the software: three geoid models (egm84, egm96, egm2008) and the ellipsoid of the selected horizontal system. For example, a project with horizontal coordinates based on the ellipsoid of WGS84 can have vertical coordinates based on the ellipsoid of WGS84 (see screenshot below) or one of the geoids (egm96 is the default option). The same applies to any other coordinate system.
If you need to select a different vertical datum such as the NAVD88, then you should either provide the offset between the desired datum and the ellipsoid of the selected horizontal coordinate system or to select the option Arbitrary for the vertical coordinate system of the outputs and the GCPs and import GCPs with coordinates in the coordinate system you specified.
In the first case, you should know the shift/offset between the current vertical coordinate system and the target vertical coordinate system (NAVD88). This shift can be added in the Geoid Height Above XXX Ellipsoid option. It might be difficult to know this shift. Even if you know it, it will only be an approximation as to convert from one system to the other, just one shift is not enough. Therefore, the vertical coordinates will not have everywhere the same accuracy.
You can find more information about when to use the Geoid Above the Ellipsoid Function here: When to use the Geoid Height Above the Ellipsoid Function?
In the second case, the software will respect the GCPs values and will try to fit the model as good as possible to the GCPs. Then, all your outputs will still be in an arbitrary reference system but this system will be based on the system defined by the GCPs. To check the accuracy of this method and see if it is suitable for your purposes you could possibly try to run a project setting the vertical coordinate system of both the GCPs and the outputs to Arbitrary and using checkpoints. The checkpoints assess the accuracy of the model.
Hopefully this helps.