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Take a look at fslmaths -- that should be all you need to manipulate the images and create masks. David -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of John Kuster Sent: Thursday, July 16, 2009 11:18 AM To: [log in to unmask] Subject: [FSL] How to create one mask using multiple ROI's Dear FSLers, I would like to take a 3d image and mask out everything but a certain number of regions of interest, all in this one mask. Is there a command that can do this? I checked here, http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html, but did not see one. Also, similarly, if I want to edit a mask to include only a ROI, or a set of ROI's how can I do that? Thanks for your time and help, Jake