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Hi Feng, The input and reference meshes are not treated in exactly the same way by flirt - it is set up with the assumption that the reference image is the higher quality one. This is the reason that you will not get exactly the same results with your method 1 and 2. In this case, you will probably want to stick with using the atlas image as reference. If you are not satisfied with the accuracy of the registratrions that you are getting, you might want to consider using nonlinear registration with an intermediate T1-weighted volume if you have it; you can use either the FDT gui or the command line tools for this. There is also the option of using nonlinear registration with the FA template, which is what TBSS does, but I am not sure that it is the best approach for other types of analyses where you might care more about GM alignment. Hope that helps! Cheers, Eelke > On 21 Jul 2015, at 03:43, chenhf_uestc <[log in to unmask]> wrote: > > Dear FSL experts, > > I want to obtain the affine matrix from MNI space to individual diffusion space. I use two methods. > > Method 1: I transform the diffusion image to standard image: > flirt -in B001_FA.nii.gz -ref FMRIB58_FA_1mm.nii.gz -omat diff2standard.mat > and then, inverse the affine matrix that from diffusion to standard: > convert_xfm -omat standard2diff2.mat -inverse diff2standard.mat > > Method 2: I transform the standard image to diffusion image: > flirt -in FMRIB58_FA_1mm.nii.gz - ref B001_FA.nii.gz -omat standard2diff.mat > > However, I found the matrix standard2diff.mat and standard2diff2.mat are not the same (attached), why? So, which one is the corrected affine matrix from standard space to individual space, and why the other is not right? > > > Any help will be greatly appreciately. > > Best, > Feng > <diff2mni.mat><mni2diff.mat><mni2diff2.mat>