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Hi, fslmaths along with the -roi flag can do this for you. Here's an example with the MNI152 fslmaths $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask.nii.gz -roi 0 45 0 109 0 91 0 1 -bin right_side -odt float Just replace the MNI152 with your bilateral mask. Cheers, Jeanette On Mon, Jul 2, 2012 at 1:46 PM, gj <[log in to unmask]> wrote: > Hi, > > Sorry newbie question...I'd like to create masks using the Harvard-Oxford > atlas because it has the subdivisions of ROIs I'd like...but the ROIs are > all bilateral. I've been using fslview to load the structures from the H-O > maps and then manually erasing one of the sides to create new unilateral > masks...but according to the 3D view and doublechecking in other displays, > I never seem to get a clean erase even though I think I'm going slice by > slice, systematically in all 3 dimensions, and increased the pixel size of > the eraser. The 3D view doesn't seem editable? Surely there is a better way > of doing this? > > Thanks a lot in advance for any advice, > g >