Hi, Clément-
Thanks for sending the data.
I don't think your alignment case calls for @animal_warper; you have basically 2 skullstripped dsets to align, after doing this:
# apply mask to F99
3dcalc \
-a F99_with_skull_mask.nii.gz \
-b F99_with_skull.nii.gz \
-expr 'a*b*step(b)' \
-prefix F99_SS.nii.gz \
-short
so my thought would be to just use 3dQwarp directly, and apply the warp to the F99-atlas you have. So, I am running this command now (note use of lpa cost function, because the NMT and F99 have similar contrasts; I chose to run it just to level 9, which I expect to be fine):
# align F99 -> NMT
3dQwarp \
-allineate \
-lpa \
-maxlev 9 \
-source F99_SS.nii.gz \
-base NMT_SS.nii.gz \
-prefix F99_in_NMT.nii.gz \
-inedge \
-allineate_opts "-autoweight -source_automask"
When that finishes running, you can warp your atlas, which is in F99 space, to NMT space with:
# also use "-master .." so the new dset is on the NMT grid
3dNwarpApply \
-nwarp "F99_in_NMT_WARP.nii.gz" \
-master NMT_SS.nii.gz \
-source RM_inF99_sp.nii.gz \
-prefix RM_inNMT.nii.gz \
-interp NN
*Note* that if the NL warp had been estimated with @SSwarper, I would have to provide *both* the WARP + *.aff12.1D matrix to be concatenated after "-nwarp .."; but 3dQwarp on its own puts the full NL warp (which already includes the affine part) into the WARP set--- the aff12.1D file is just for the first step alone.
... and the final alignment looks good-- attached is an image of the F99 warped in NMT space, overlaying the (edgified) NMT template.
--pt
