Hi, Momo-

Glad the program is useful for the mouse applications, too.

There are a lot of intermediate warps that you wouldn't need to use. To go from "input" to the base dset with warps that have been created, you should be able to use the same warp information that is provided to afni_proc.py:

*_composite_linear_to_template.1D  
*_shft_WARP.nii.gz

... and you should be able to apply these as follows to your original input dset INPUT_DSET, to send it to the same space as your reference dset REF_DSET:

3dNwarpApply \
    -master REF_DSET \
    -source INPUT_DSET \
    -nwarp  "*_shft_WARP.nii.gz   *_composite_linear_to_template.1D"
    -prefix INPUT_IN_REF.nii.gz

(Note: I wouldn't actually use the asterisks in the above command, but probably the real file name.)

Does that work for you?

And just to check, as well-- what version of AFNI are you using (i.e., the output of "afni -ver")? The @animal_warper program has changed a bit over time-- I would just like to verify that you have a modern one.

Also, it's not clear to me what you mean by "annotations". Note that when you run @animal_warper, you can include several other datasets to "follow" the warping, either atlases/segmentations or float-valued dsets; and those can be either in the template space (and hence get warped to the original input dset space) or in the original input space (and hence get warped to the template).

--pt