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I am not familiar with the converter you are talking about, but please have in mind that fuzzylite provides more features than Matlab’s toolbox, for which there are some keywords that are not supported by Matlab and issues occur when importing with them. Specifically, you will need to remove the following keywords from the fis files that are exported using qtfuzzylite:
Please, make sure these lines are not present in the fis files before using your converter. Let me know if this works for you.