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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