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Hi again,I think the best thing would be to try to get the brain extraction working better on your b0 images. If you aren't correcting for geometric distortions with a field map, then that may potentially have an impact but it's likely that there is still a way to get a reasonable brain extraction regardless. If you want to send me a sample b0 image or two, I can try to take a look. I might not get to it until tomorrow though.If you want to proceed with your original idea, then you should just be able to apply the registrations from the FA images to your b0 masks.Hi Neil,I apologize for the confusion. "bunch of BET images" was not correct. I used BET to create a ' binary mask' of the brain tissue from b0 images. BET usually does not very well on my b0 images and most of the time parts of the brain tissue is chopped off or other not brain stuff is included.I have already transformed the FA maps from individual space to a common space. Is it a good idea to use those transformation matrices to register each binary mask from an individual space to that common space and the average them?Thank you!MahmoudOn Thu, Jan 12, 2017 at 11:53 AM, Niels Bergsland <[log in to unmask]> wrote: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,MahmoudOn 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,NielsNiels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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