Need help in using OpenDroneMap for stitching images (getting orthophoto)

Hey i am new to opendronemap want to learn how to stitch images

i am using images from

i tried merging few images i am getting holes in image (seems like i am doing something wrong)

what should be the best setting to get best orthophoto

Bigger picture of what i am doing:
i am doing segmentation of images into (road , vegetation ,houses) ,i am able to do that for all images (individually )
can you guys guide me how can i merge these segmentation masks to orthophoto .
may be i need projection matrix (homography matrix for each image) ,is there an option to get these in ODM