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Hi Stefano, > we are running some sample data through the FSL pipeline for distortion correction and have a few questions. > We ran top-up on our b=0 images and wanted to feed the results to eddy, but we don't have a guide on the FSL website yet. Could you please send an example of the command line? I assume something like: > eddy --imain=DWIseries --mask=brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=topup_output --out=eddy_out I'll update the online documentation later today. > > We have also acquired phase-up and down for all the diffusion volumes we have. What is your experience on this point? Is it better to run top-up on each individual image or to just apply the b=0 warp? Any detail on this issue would be useful. I suggest just applying the b=0 warp. You are feeding the topup results into eddy, which means that the b=0 field is used in there as a "starting point" for each dwi and then that is refined with a low dof non-linear eddy current field for each dwi. > Finally, does eddy rotate the b-matrix according to the movement of the head? No it doesn't. Jesper > > Stefano Marenco, MD > NIMH/CBDB > 10 Center Drive, Bldg 10 room 3C103 > Bethesda MD 20892 > Tel 301 435-8964 > Fax 301 480-7795 > Email: [log in to unmask] >