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Hi, I'm confused about this flirt command as described in the FNIRT user guide: flirt -ref my_betted_structural -in my_functional -dof 6 -omat func2struct.mat My understanding of coregistration is that we take a representative functional image (eg the mean image of motion correction step) and use it as the stationary (reference) image. We then take the anatomical image (the input image) and we move it to align it to the mean functional image. Assuming that my_functional.nii.gz in the example above is motion corrected (eg the mean image of motion correction), why would I select the structural image as the reference image, and the my_functional as the input image? Won't this jiggle about the motion corrected functional image to match the anatomical image, which would defeat the purpose of motion correction? Thanks! Ben ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1