Hi,

There may be a simpler way, but off hand, you could do something like this

cluter -i input -t 0.01 --osize=sizeim

fslmaths sizeim -thr THRESH -bin mask

adjusting the THRESH parameter as necessary to remove the clusters made up of a small number of voxels.

On Sun, Feb 12, 2017 at 3:05 PM, Eric HG <[log in to unmask]> wrote:

Hi everyone,

I'm currently trying to create a ventricle mask using fslmaths. However, I keep getting a mask with just a few single voxels in brain and I was wondering if there is a function in FSL that can remove voxels without "neighbours"?

I've already tried erosion in fslmaths but it removes too many voxels.

Best,

Eric

Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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