Pix4D will generate shapefiles as lines, while SMS software expects polygons. This means that an extra conversion step is necessary to make the Pix4D .shp file ready to be imported in SMS AgLeader.
One way is to proceed is to use QGIS. After having imported the shapefile, one can click Vector>Geometry Tools> Lines to Polygons and save the polygon shapefile. This file can now be imported in SMS AgLeader.