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Hi, It is a little more complicated than that - especially given that images can have either left-handed or right-handed coordinate systems. To find out how coordinates map between spaces use the utilities img2imgcoord, img2stdcoord or std2imgcoord. All the best, Mark On 9 Feb 2009, at 21:43, Xiuyuan Wang wrote: > Dear FSL members: > > I was working on the brain registration on FSL 4.0 FLIRT. It did a > really good job when I coregistered the post operation MRI image > with the MNI standard one using DOF 12, and it gave me a 4*4 > transform matrix from post operation space to MNI space. What I want > to know is: how does the flirt work on a single voxel? Is it just > the multiplication of the transform matrix and [x;y;z;1] (x, y, z > are the voxel positions in post operation space) ? Thank you. > > Best, > Hugh