Thanks a lot Daniel, that worked!
Also, just as a note for anybody trying to do similar stuff, I ended up doing a dummy pass of 3dNwarpApply (3dNwarpApply -prefix $out -nwarp 'IDENT(session1+orig)' -master session1+orig -source session1+orig -interp NN) on everything before doing anything else. I started doing that sometime ago after encountering problems using 3dNwarpApply to apply all my preprocessing in one steps. 3dNwarpApply seemed to change something in the header that affected slice position, which was problem for me who is not deobliquing and incorporating fsl and freesurfer tools. The dummy pass allowed this change to happen the very beginning and seems to prevent funny things to happen later.
Cheers
Sébastien