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Hi! First you might want to stack both together and run eddy_correct on it. After you might want to average each volume_1 with the corresponding volume_2 by using: fslmaths volume_1 -add volume_2 -div 2 averagevolume -odt float You might want to organise this in a loop over every volume 1:end Hope that helps, Markus 2009/2/18 Deryk Beal <[log in to unmask]> > Hello FSL Community > > We have acquired 2 runs of diffusion images for each of our participants. > We > would like to average the 2 runs together before further analysis. Is there > an FSL tool or protocol that we can use to do this? > > Deryk > -- Dr. med. Markus Gschwind, M.D. Laboratory for Neurology and Imaging of Cognition Dept of Neurosciences University Medical Center (CMU) 1 Michel-Servet - 1211 GENEVA - CH Tel 0041 (0) 22 379 5324 Fax 0041 (0) 22 379 5402 email: [log in to unmask] http://labnic.unige.ch