Try also with GMT.exe to split mapset with given FID and map name:
gmt -S -f 5000,1 -m "New map name" map.img
error that gmaptool gives means, that it cant choose by itself which FID/PID and map name to use
When img contains single map, gmaptool use FID and map name from this map. when they are multiple maps, you need to give this values explicit
Mapsource will accept any FID/PID, even different then real FID of the map.
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