Hi Ben,

Some screenshots would be helpful in diagnosing the problem - overlay reg_img.nii.gz on top of T1.nii.gz to check the quality of the registration.

What are the contents of the transformation matrix that FLIRT generated?

On 29 August 2018 at 20:11, Ben M <[log in to unmask]> wrote:
Hi Matthew,

Thank you very much for your reply. I included the -omat flag and got the transformation matrix but I'm not sure what I can do to check if the image is being transformed correctly. What would the standard procedure be to check if the registration was successful?

Best,
Ben

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