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> > Strange - this must be a platform-dependent bug, as it works fine on my > mactop, and gives good results too. What platform are you using? > > However, anyway: the attached script eddy_correct (which will be part > of > FDT, the diffusion toolkit, when it's released later this summer) uses > FLIRT instead of mcflirt to realign diffusion data, the point being > that > when you have eddy currents you need affine alignment not rigid body, > which is more of an issue with diff data...you might want to try that > instead, though on this data it seems to give similar results. > > Cheers. > Steve, thanks for the script. I'm running on linux (suse 9.0). What I was doing was first using mcflirt to realign the individual runs separately for each diffusion direction (we generally collect 4-5 runs), taking the mean for each direction, then using flirt with 12 dof and mutual information to align across the different diffusion directions. Does that sound reasonable? The data that I sent were all for a single direction, which is presumably why the results of flirt and mcflirt are similar. cheers russ --- Russell A. Poldrack, Ph.D. Assistant Professor of Psychology, UCLA Franz Hall, Box 951563 Los Angeles, CA 90095-1563 email: [log in to unmask] phone: 310.794.1224 fax: 310.206.5895 web: http://www.poldracklab.org/