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Hi, Once you've selected the region that you want and have the appropriate intensity value, you can do the following in fslmaths to extract the relevant region: fslmaths atlasimage -thr VAL -uthr VAL -bin binaryregion where VAL is the intensity value of the region you want. The output image (binaryregion) is a binary mask of that region. Note that some of the atlases also have a 4D image that stores a probability map for each region separately. In that case you just need to work out what volume it is in and then use fslroi to extract just that volume. Hope this helps. All the best, Mark On 16 Mar 2009, at 21:07, Jennifer Bramen wrote: > Dear FSL List > > I would like to use individual regions of interest from one of the > free atlases. However, the > atlases are composed of multiple regions and I do not know how to > create a separate mask > for an individual region. Is there a command I can use? > > Thanks > > jen >