phantom Vision+ v h3-3d with go pro and use with pix4d

I recommend trying the same image set in Agisoft Photoscan.

Either way, if you want commercial level results you're probably going to want more RAM.
 
Nice =).

About the SD card error, unfortunately, you cannot bypass it by now. Also, there would be other problems later in the mission. Unfortunately I don't have such a hybrid system, so I cannot test it =/. Maybe one day I will have time to do it for fun!

Otherwise you can still fly manually, as you did. Try to make the camera look downwards (we call this "Nadir") and fly in parallel lines (with an altitude of, say, 50m, you can fly in lines separated by around 20m). Then it is a trial-and-error process to get experience about how to fly in a good way for reconstructions. Also, you should remove the "bad" images (such as the one during the takeoff, where you don't really see the scene).

Cheers
 
Jonas's description of the Nadir is a little simplistic.

You want to be on a 90 degree angle, more or less from anything you're shooting. Say you're scanning a lighthouse; you want to be facing towards it's walls on a horizontal level, while circling it, looking in.
 
Maybe that wasn't perfectly clear indeed. Thanks for the precision ;-).

In Pix4Dmapper Capture, the automatic mission is always taking pictures from an altitude of 50m, usually looking downwards (but you can modify this in the settings).
For a lighthouse, you will need the "Free Flight" mode, and set the camera angle accordingly.
 

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