Dear fsl users
I want to betpremask (through standard_space_roi) my data in order to do
longitudinal and cross sectional analysis with siena and sienax respectively.
Since siena needs the skulls of the original images i can't just do a shell
script that sends as inputs to siena the stripped brain images after
betpremasking them. I've read in FSL forum that it's better to change the
siena script as follows: "leave BET to extract the skulls, then run
betpremask and feed, then run again bet on the premasked images and feed
siena with these results." The problem is that siena script is too
complicated for my scripting skills and i would really appreciate if you
could tell me how to change this script in order to betpremask my data first
(bet_robust totally fails in most of my data which contain big protions of
neck even if i determine the COG with the -c option.That's why i need
betpremask since it gives me really good results).I use the fsl 4.0 version
on ubuntu platform.
How about sienax ? it also needs the skulls in order to register the images
with pairreg? How the sienax script should be changed in order to
incorporate betpremasking?In this case also, a shell script that sends as
inputs to sienax the betpremasked images wouldn't work..Right?
Thank's a lot for your time
Antonios-Constantine Thanellas
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