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Just thought about using the first volume as the reference volume: !$FSLDIR/bin/mcflirt -in slice1 -refvol 0 -mats -plots This also seems to help the correction; does this make sense? !$FSLDIR/bin/fsl_regfilt -i slice1_mcf.nii.gz -d slice1_mcf.par -o slice1_mc_regressed.nii.gz -f "1,2,3,4,5,6" I now need to know the transform from slice1 to slice1_mc_regressed to apply to real and imag images. I saw this message from Mark back in 2011: I'm afraid applywarp will only take one matrix at a time. The tool applyxfm4D would take a set of matrix files, but unfortunately does not yet support spline interpolation. We will be putting spline interpolation into these tools in the future though, but at the moment you need to do fslsplit, loop applywarp, then fslmerge. I assume applyxfm4D still doesn't work with spline? Cheers, Lucy