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Thanks, Doug. I think the command is MCFLIRT. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT
Best Wishes,Shane On Friday, May 3, 2019, 6:18:54 PM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane