Hello all
I am currently using Siena to process two time points longitudinal data. As we modified Siena that allows us to set two different parameters for BET function. However the results showed frontal lobe and top of the head are chopped off in the FAST, PBVC and halfway results when the BET results shows no problem at all.
I thought this may be caused by coordinate for central of initial brain allocating option "-c" in BET as our data have quite different central coordinate. (e.g. For the subject result I attached, -B1 "-c 132 64 134.5" -B2 "-c 130 121.5 93"). But I discovered that if I use rubost brain central estimation or Eye & optic nerve cleanup or Bias field & neck cleanup BET function, the coordination for certal initial image does not affect BET results, but I do not know if this coordinate would influnce other sub functions in Siena. As there are limited online resources to check for resolution. Would any of FSL experts in the list please let me know if there is anything or parameters could correct such error? Thank you inadvance.
I attached the images I have got for one subject as example.
Joyce
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