OHBM? Chaotic? Suuuurely not... Well maybe just due to us being here.

Re. the link---Aaaaah, now I see the issue. The initial link you posted just appears to actually be the main AFNI MB page (judging by hovering over it). This more recent one does appear to be something more specific that kinda resolves to something more specific, but then falls back to the main page. Where is it supposed to go? Somewhere in this thread, or to a different thread?

Re. the warping: thanks for posting that image. It points out that it doesn't appear that you are using SSwarper to align a whole brain dset (e.g., subject anatomical) to the MNI template. The underlay looks like just a single ROI. Is that the case? @SSwarper's input needs to be a subject anatomical, basically.

Instead of putting the ROI there as input, you woudl want to put the template that contains that ROI (e.g., the TT_N27 dset or something), and use a nonlinear alignment program to align that to the MNI space (in this case, probably 3dQwarp or auto_warp.py directly, because both dsets are already skullstripped). Then, you would apply the estimated warp to the ROI dset, with NN resampling, to keep the ROI "ROI-like".

Does that seem fine to do?

For example (and I am theorizing this while at the conference, not fully running it to verify first...):

# estimate warp
3dQwarp -source DSET_TEMPLATE_TALAIRACH   \
              -base   DSET_TEMPLATE_ MNI     \
         -prefix dset_tlrc_in_mni             \
        -lpa                                 \
        -allineate                           \
        -allineate_opts "-twopass"

# apply_warp (note that the *.aff12.1D affine part should not be included separately here--it is part of the 3dQwarp output's WARP dset already)
3dNwarpApply -nwarp  dset_tlrc_in_mni_WARP+tlrc.HEAD  \
               -source DSET_ROI_TALAIRACH         \
               -prefix dset_roi_in_mni

Please let us know how that sounds/runs.

--pt