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.

On 1 Sep 2014, at 18:57, Rosalia Dacosta Aguayo <[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.