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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