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Hi Niels, Thank you so much for your explanation. My concern is that I don't know how much different is registering a binary mask from registering a structural image. In the latter, there are some many details that might be used for the registration while there is not much info in a binary mask so I thought there might be a specific way to register binary masks. About the goal of doing this registration: I have BET images in individual space. Those images are not perfect. I want to register all the images into a common space and then average the registered BET images to see what areas of the brain mostly chopped off. Thank you, Mahmoud On Thu, Jan 12, 2017 at 11:30 AM, Niels Bergsland <[log in to unmask]> wrote: > Hi, > Sorry about that - I read your email too quickly and didn't notice that > you were not just doing a straight subsampling. There is a section on this > in the FLIRT FAQ (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ), > particularly the last paragraph of Can I register to an image but use > higher/lower resolution (voxel size)?" section. > > If you have access to freesurfer, you may find that this is easier to do > with mri_convert, in that case you can do it like this: > > mri_convert -vs 2 2 2 -oni 92 -onj 92 -onk 56 INPUT.nii.gz OUTPUT.nii.gz > > > Regarding your other question, it's difficult to say without knowing more > about exactly what you're trying to do but in general, you would do > something like an affine registration with FLIRT and then a nonlinear > registration with FNIRT. There are some basic examples of this on the FNIRT > webpage. > > Hope this helps, > Niels > > > > >