I had a similar problem. But using standard_space_roi before BET
helped a lot. See my blog entry here
http://neuroimager.wordpress.com/2012/10/26/brain-extraction-using-fsl-bet/
about its usage.
m-
On Fri, Nov 2, 2012 at 5:47 AM, Catherine Tang <[log in to unmask]> wrote:
> Dear All,
>
> I have a set of T1 data, which needs to use BET....however, so far I have tried 4 subjects, only one seems to work great after I adjust the f value...
>
> the other three data, no matter how i change the f value, the data still got a lot of grey matter cut off after BET...
>
> I used the bias field and neck clean up option, and i also tried bet2... it still does not work.. i have tried to attach one t1 file in the email, but for some reason the message never got posted on the list...i was wondering if it is because of the large file I attached. Instead, i attached a picture to show what is going on.
>
> Hope someone could give some suggestion on how to solve this issue.
>
>
> Thanks a lot,
> Catherine
|