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Hi Mahmoud, You are absolutely right about trying to register a binary mask - and you can't directly register it. You need to do the registration using the corresponding structural image and then apply the transformations to your masks. I'm still a little bit confused though. You mentioned in the earlier email "bunch of BET images" but now it seems like you're referring to binary masks? I thought you were referring to brain extracted images. If you want to register the binary masks, you should use the corresponding structural image. Once you've gotten all of your masks into the same space, you can certainly make an average image. If there's something that I've misunderstood, let me know. On Thu, Jan 12, 2017 at 5:43 PM, Mahmoud <[log in to unmask]> wrote: > 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 >> >> >> >> >> > -- Niels Bergsland Integration Director Buffalo Neuroimaging Analysis Center 100 High St. Buffalo NY 14203 [log in to unmask]