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Hi Matt, These commands are the right thing to do. The reference volume should be the size and resolution of your desired output. Typically for unwarping an EPI you'd take the same image as the reference, thus keeping the FOV and resolution the same. You need the shiftdir for the convertwarp call but you don't need it in the fugue call if all you are doing is making a shiftmap (which is a scalar image). I would recommend using the fieldmap if you've already made it. All the best, Mark On 20 Jul 2010, at 23:01, Matt Glasser wrote: > Hi, > > I want to convert a field map to a warpfield (suitable to be used > with convertwarp and applywarp) so that I can concatenate it with > other warpfields and affine matrices for a one step resampling with > applywarp. I see that fugue can output a shiftmap and convertwarp > can convert a shiftmap to a warpfield. > > Lets say I have a field map that is working fine to correct > distorted EPI data, will the following work to get what I want: > > fugue --loadfmap=<field map in rad/s> --dwell=0.000590 -- > unwarpdir=y- --saveshift=<shift map> > convertwarp --ref=<reference volume> --shiftmap=<shift map> -- > shiftdir=y- --out=<warp> > > What should the reference volume be? Do I need to specify the > direction of the warp in the fugue line, the convertwarp line, > both? Is it okay to use the field map and not the phase map (since > I already have made the field map)? > > Thanks for any help, > > Matt.