bbregister will compute the matrix, you don't have to give it a matrix. You can use mri_vol2vol to apply the matrix. There is also an option to apply the matrix in bbregister

On 1/31/2022 7:24 AM, m-maiworm@web.de wrote:

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Hi, I ran recon-all on a MPRAGE-file, which was registered in freesurfer-space. Now I want to register other sequences like T2 in the same space using the registration matrix. What is the best way to do this? In bbregister I didn't found an option to give the registration matrix which should be used, so applywarp would be an alternative, but I'm not sure which files I should name in --warp and --premat.

Can somebody help? Thanks! Michelle

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