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Dear David, If I understand your email correctly (as I found it a little confusing) you have an image in MNI space (i.e. normalised) and you want to resample this to match the FSL MNI space template? If so then you can use the -usesqform option in FLIRT, instead of the -init, with the -applyxfm option in order to achieve the resampling based on the MNI coordinates. That is: flirt -in TheSPMimage -ref TheFSLtemplate -applyxfm -usesqform -out ResampledSPMimage All the best, Mark On 8 Jan 2014, at 13:42, David Soto <[log in to unmask]> wrote: > hello, I have not got round to display in FSLview a cluster > mask which was normalised in a old SPM analyses. > we have played with the mask using fslswapdim and also > doing flirt again without success, does anyone > have any advise on this? > thanks! > david