I have found that reducing the radius (-r option)
of the initial sphere allows you to properly extract monkey brains with
BET. I used 50mm for my successful extractions, but you should measure
the radius of your brains and use whatever value you find. Also make sure
the center of gravity (-c option) actually is in the center of the brain.
Peace,
Matt.
Dear FSL users,
We have acquired two MRIs from the same monkeys (vervet) before and after
treatment.
SIENA seems to
be the right tool to investigate possible structural changes caused by the
treatment.
Since the monkey MRIs could not be acquired like human MRIs in terms of AC-PC
alignment, I processed the MRIs in such way that the resliced image is
AC-PC aligned (using SPM2 display and reslicing tools).
According to my preliminary run using SIENA,
it looks like BET fails to extract the brain tissue.
I will appreciate any comments for the following two questions.
1. Can I use SIENA
in monkey MRI analysis?
2. Are there any specific changes of the options that I can try in BET so that
the brain tissue can be extracted correctly?
Thank you,
Buyean
