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I have two mosaics taken in different band sets respectively, on two different flights- of a crop field. The flights were taken a day apart, so the vegetation cover has not changed. The only issue is the shadows, and slight distortions between the mosaics - as they were stitched from UAV imagery.

I tried georeferencing one to the other in QGIS 2.18; however, there is still slight offset which makes the creation of indices problematic.

How can I get a more accurate pixel to pixel alignment using QGIS?

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