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I think I may know what will work, but in the end you can check and see if this is what you are looking for. Use the flirt with three steps (low->high->ref). Use Affine (12 parameter model) to register the high res to the reference. This is because you need to use all the degrees of freedom to transform your subject's highres image into reference space (these are very different brains). Use the Rigid body (6 parameter model) for the lowres to highres transformation (they only need a little shifting since they are the same brain). Once this is complete, you will have 3 transformation matrices. I believe they are numbered in the following way: low2ref.mat = lowres to standard; low2ref1.mat = highres to standard; low2ref2.mat = lowres to highres. Now you have all the transformation matrices that you should need for the rest of your analyses. Take the matrix that transforms from lowres to highres space and invert it using invert flirt transform in the utilities. Now you want to apply this matrix, which is highres to lowres, to your T1. You may actually want to draw your masks in highres space and then apply the inverted matrix to the masks instead. See what works for you though. I am pretty sure this is what I have been doing and it has been working with good results. ted On Jan 19, 2008 10:39 AM, Jiansong Xu <[log in to unmask]> wrote: > Dear Friends: > > I'm trying to define ROIs during analysis of DTI data, and find that > the resolution of both B0 and FA images are too low. I want to co- > register T1 and B0 and FA map, so that I can take the advantage of > high resolution of T1 image and define ROI on T1 image of each subject. > > I used Flirt with Rigid Body (3 parameter model) to co-register the T1 > with either B0 or FA map of the same subject, but the result was not > good. I'm wondering if anyone can make suggestions. > > Best > > Jiansong >