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The main difference is that you will have to set the shot point byte position for both inline and crossline in the 3D import, while in 2D there is of course only one shot point column. The 2D import also has a Analyze panel that lets you fix anomalies in the SEG-Y file.
Another difference is that for 3D import you can choose how the seismic cube will be stored within the Geocap project; either in the new brick format (default) or in the older Vtk format.
For more information about the SEG-Y format, see the SEG page SEG-Y standard: http://www.seg.org/resources/publications/misc/technical-standards
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