IW3D_invert convergence warning when using intermediate outputs from sswarper2

[ptaylor]

Hi-

That warning is probably OK to ignore, if the results look good on the other side. There might have been a tiny spot that didn't converge, possibly even at the edge or outside the brain.

Note that this discussion provides a more modern model for using+inverting @SSwarper or the newer/recommended sswarper2:

use Schaefer atlas in subject space

Hi, Maya- I'll assume this refers to volumetric alignment (the S-Y atlas is defined on surface meshes as well, which transfer to subject space meshes directly if using SUMA-standardized ones). This process will likely involve running nonlinear alignment between each subject's anatomical volume and the template on which the Schaefer-Yeo atlas is defined. If the errts itself is living in the anatomical volume space, then that would be all that is necessary (that is, if the "align" block were u…

The difference is in the order of concatenating the nonlinear warp with the affine transform part and inverting the warp. 3dQwarp's warps are diffeomorphic, and hence invertible; but if concatenation happens first, that beast might not be smoothly invertible in some places. So, it is preferable to invert each piece first, and then concatenate those parts. Namely, for applying the inverse warp to an integer-valued dataset, use:

# create the inverse transform from sswarper2 and apply it to atlas in template space
3dNwarpApply                                                        \
      -nwarp  "INV(${odir}/anatQQ.${subj}.aff12.1D)                 \
               INV(${odir}/anatQQ.${subj}_WARP.nii)"                \
      -ainterp NN                                                   \
      -master "${dset_in_native_anatomical_space}"                  \
      -source "${dset_in_template_space}"                           \
      -prefix DSET_OUT

(If your "source" dataset is not integer valued, you can leave out the -ainterp NN or even keep it and replace "NN" with something like "wsinc5".)

--pt