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Contours and Imagery Not Lining Up

When I create contours in Pix4D I am creating them as 1-foot contours both DSM and DTM and export in a .dxf format.  I bring the contours into Microstation V8.  I then bring in the orthomosaic created from the same Pix4D project.  However, each time I do, Microstation shows the contours offset from the imagery.  This is not the case if I bring the same data into GIS (they line up perfect).  I also tried bringing the data into Global Mapper and the data was offset even worse.  Global Mapper also indicated that the contour data had no projection assigned to it.  However, the imagery does have a projection.  I’m thinking that each software is trying to reproject the contour data into whatever coordinate system is set by the ortho but not doing a very good job of it. Any thoughts?

Hello Henry,

The contour lines that are generated by Pix4D are georeferenced and they refer to the selected output coordinate system, the same as the rest of the Pix4D outputs. 
What kind of offset do you observe? Is it horizontal, vertical or in both directions?

Are you using the .dxf file for the Microstation V8 and the GIS software? Or are you maybe using the shapefile for GIS?
Could you please post here the quality report of the project and share with us the contour lines and the DSM/DTM files?