Hi Ben,
Normally, I use fslroi to extract the voxels of interest. After that I
use FLIRT (6 DOF) to register the images to a standard template. I
have found that this pre-processing yields very good results with BET
thereafter (less neck).
Cheers,
Benny
2008/9/26, Ben Yerys <[log in to unmask]>:
> Hi List--
>
> I'm running the VBM analysis with three groups (n=15 per group), and I ran
> fslvbm_1_bet with the -n option. The extraction worked well for 44/45
> participants, but included a substantial portion of the neck as brain in one
> child. Should I remove 3 children (one from each group) before creating the
> template in step 2? Or is there another way to salvage this participant's data?
>
> Thanks,
> Ben
>
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