Greetings,

The SIENA program only allows me to specify one BET fractional intensity threshold for two images. My two images require different intensity thresholds. After completing BET, I would also like to perform an intensity correction procedure on the two images before running the rest of the SIENA protocol.

Is there a way to by-pass the BET step in SIENA and do it myself separately, then do the intensity correction, and then run the rest of the SIENA protocol (e.g., siena_flirt, siena_diff) on these two intensity corrected brain images? I have tried to run siena_flirt with my two intensity corrected images and I get an error message because my images are not "A" and "B." What steps should I take after completing the BET and intensity correction so that I can complete the SIENA procedure (co-registration, segmentation, and analysis)?

Thanks,
Abbey