Hi, I would avoid using nearestneighbour in this case, and instead use trilinear and then threshold the output appropriately (which is probably going to be a small threshold, as your mask is probably thin if it is disappearing). Have a look at the result from the trilinear resampling to get a feeling for what would be an appropriate threshold. All the best, Mark On 1 Sep 2014, at 18:57, Rosalia Dacosta Aguayo <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL experts, I am trying to resample a binarized mask that it is in MNI space with 2mm of resolution to 4mm resolution in the same MNI space. What I have done is use ApplyXFM with the following flags: ApplyXFM applyxfm -init /usr/share/fsl/5.0/etc/flirtsch/ident.mat -out GROUP_VOI_4mm -paddingsize 0.0 -interp nearestneighbour -ref GROUP_VOI_4mm_tmp The problem is that I can see the mask in 2mm MNI space but when I do the resampling...the mask disappears!!! Any suggestion? Best regards, Rosalia.