It is worth trying FIRST and seeing how well it performs.
There is quite a range of brains that have been used in the
training, so there is a reasonable likelihood of good segmentations
provided that your brains are not too extreme.
As for the command - the syntax looks fine. Are you using
the most up-to-date version of FSL? It sounds like you are
using an old version. Just update your version and try again.
All the best,
On 31 Jul 2009, at 21:19, Balint Alkonyi wrote:
> I`d like to segment thalamus and hippocampus from brains of some
> sturge-weber syndrome patients, whose one hemisphere is atrophyc in
> cases. Is it feasible to run FIRST on these patients at all. Their
> brain is
> much different than the MNI template...
> I tried to type a command `run_first_all -i hamon_brain -o
> -s R_Thal -b` on a brain extracted analyze image (hamon_brain). It
> failed to
> do the process and said that -s is an invalid option.
> What command should I run if, let`s say I want to extract the right
> Can someone help with straightforward commands?