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I also need to know how you get to a rad/s image. Is the "phase" image you sent actually a phase difference image? And if so, what is the echo time difference that you use to convert it into a rad/s image? I suspect that your problems are probably due to the thick voxel size in the z direction (four times that of the x or y voxel size) and the fact that the fieldmaps themselves also seem distorted (e.g. ventral portion of the brain in slice z=4). If you give me the above information I can run fugue for you and send you the results. I will also find it difficult to assess the results as I'm not that familiar with mouse brains and I don't have a non-distorted image to compare it to. If you also had a structural image that was not distorted then that would help me too. All the best, Mark On 9 Mar 2011, at 08:21, Van Lee wrote: > Hi thanks. I used the full-skull one, because I cannot extract the brain from the skull. Maybe because of that, it failed? > > Btw, the dwell time is 0.0003s and the TE is 43ms. > > Thanks a lot! > > Van L >