For those of you addicted to Matlab, mgstat may offer the solution you need. It is a matlab package developed by Prof Thomas Mejer at the Niels Bohr Institute in Denmark. The package has its own structure to store the parameters and data from Matlab, call SGeMS from the command line and seamlessly import the results back in Matlab. A very well made tool set.
If you have questions about mgstat, please post them in the User Forum, Prof Mejer is interested in suggestions and willing to help.