I don't quite understand why it takes 40 seconds to run that script - it's not that complicated. Unless it has to do with the file reading/writing. As it stands, the code in the script is a good candidate for conversion to LabVIEW. Most of what you do in the script is looping, and this can be handled in LabVIEW using the polymorphic nature of functions - i.e., without loops.
That said, I don't see any code that sorrounds this. You mention a sequence structure, but it's not clear where that's supposed to go. I don't see an overall loop, so only the loop you show will run continously. As it stands, the Matlab script will only run once. If that's what it's supposed to do (i.e., run the script and then go into the loop), then you can just wire the outputs of the script node into the while loop. But, as I said, I really think you should convert that Matlab script to LabVIEW code.
