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flirt, and I have a lot of files to work with. So, it is taking a lot of time. I Therefore, if you used an MNI template for your normalization (FSL, ANTS)  (FLIRT), get rid of the voxels without any detectable signals, and combine Registered the individual functional images to MNI template with affine matrix from 
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D WM from MNI to FLAIR registration with  accelerating neuroimage registration through parallel A spatially unbiased atlas for the cerbellum and brainstem MNI coordinates determined using SPM2 and FSL/FLIRT with the ICBM normalization auto
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