Hi,
These commands will do what you want:
fslmaths baseimage -mul 0 -add 1 -roi 44 1 68 1 40 1 0 1 -kernel sphere 3 -fmean sphmask -odt float
fslmaths sphmask -mul 2 -thr `fslstats sphmask -p 100` -bin -mas brain_mask sphmask
You need to change the voxel coordinates (44,68,40) and there sphere radius (3) above to suit your needs. It also requires a "baseimage" in whatever space you are working in (and suits the voxel coordinates that you are using). Also, it assumes you have a "brain_mask" image (a binary brain mask).
All the best,
Mark
> On 11 Sep 2017, at 10:15, Navot Naor <[log in to unmask]> wrote:
>
> Hi all,
>
> Small question,
> Is there a way to mask a sphere based mask created based on coordinates, so that the sphere includes only regions within the brain?
>
> Thank you!
>
> Navot
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