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Hi Anthony, > > I am not sure how fnirted_A (output image from fnirt) should look > like for it appears as a mixture of squares of different > intensities. It doesn't look like a brain image but does seem to > cover the shape of a brain. It is not see easy to interpret fnirted_A, since it is a 4D file of spline coefficients. If you want to check if fnirt did OK you are better off looking at what the warped image looks like. You can do that with applywarp --ref=MNI152_T1_2mm --in=A --warp=fnirted_A -- out=A_InSpaceOf_MNI and then use fslview to look at A_InSpaceOf_MNI. If that looks good fnirt probably did alright. Good luck Jesper