Hello folks,
I have a problem with @auto_tlrc. I'm relatively new to AFNI, so I might just overlook something. When I'm trying to align the subject's anatomical to some template (no matter whether TT_N27+tlrc, TT_ICBM452+tlrc, etc.), I get very poor results, i.e., the transformed anatomical is too large and generally does not line up appropriately with the template.
I tried to follow the recommendations from @auto_tlrc -help but nothing really helped. This is one example of the many options I ran:

@Align_Centers -base TT_icbm452+tlrc -dset anat+orig
@auto_tlrc \
-base ${templDir}/TT_icbm452+tlrc \
-suffix _icbm452 \
-input anat_shft+orig \
-ok_notice \
-xform shift_rotate_scale

My best guess is that the skull stripping doesn't work very well - at least, I don't get satisfactory results when I try to do it separately (using 3dSkullStrip). Any ideas/suggestions would be greatly appreciated!
Thanks,
Kerstin