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I've installed hector_slam via apt-get, so the package is on /opt/ros/DISTRO/share path (mine was indigo). In this case, I've had to recursively change hector_geotiff's folder owner because savegeotiff command had no permission to generate *.tif and *.tfw files. Another issue was referred maps folder missing on my installation, so I've had to manually create it.

So if you:

sudo apt-get install ros-DISTRO-hector-slam

then:

sudo chown -R USER:GROUP /opt/ros/DISTRO/share/hector_geotiff

If maps folder is missing:

mkdir /opt/ros/DISTRO/share/hector_geotiff/maps

Run again (while hector_slam launch and bag are running too):

rostopic pub syscommand std_msgs/String "savegeotiff"