 |
 |
Hi, This is a good answer but I want to clarify one point - the fieldmap and the fieldmap magnitude should be undistorted images. So if you are using topup to create your fieldmap then use the undistorted magnitude image that is produced by topup for the fieldmap magnitude and not one of the original inputs to topup (as the inputs contain distortion). All the best, Mark > On 17 Mar 2018, at 04:45, Forrest Koch <[log in to unmask]> wrote: > > Hi Erik, > > I'm not part of the FSL team and I am fairly new to using FSL myself (so take my advice with a grain of salt), but my understanding is that the fmap parameter of epi_reg should be the field map produced by the --fout option of topup. The fmapmag/brain parameters should be one of the b0 magnitude images you used to produce the field map. The former being the whole brain image, and the latter being the brain extracted output of bet. > > Perhaps have a read though https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#Selected_parameters_explained and https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg > > Regards, > Forrest