title          :: Alignment (part 4/4): anatomical-template (cross subject)
presentation   :: afni14_alignment.pdf
scripts        :: 
date           :: 2020-03
speaker        :: Taylor
outline        :: 
Anatomical-template alignment, or, more generally, nonlinear (NL) warping
    + use NL warping to align to a template (really between *any* different subjs)
3dQwarp is the general purpose workhorse for nonlinear alignment in AFNI
A newer program wraps around it, combining warping with skullstripping: @SSwarper
    + combining skullstripping with NL warping improves both
For animal studies, @animal_warper also combines skullstripping+NL alignment
NL alignment is slow(ish), but can be sped up using multiple CPUs
    + AFNI's alignment programs are written with OpenMP parallelization
    + set OMP_NUM_THREADS environment variable to specify CPU usage
When choosing a template for NL alignment:
    + choose one with lots of detail (NL alignment wants to latch onto details!)
    + choose one relevant to your group (i.e., pediatric template for study on kids)
    + see other AFNI Bootcamp talk on templates and atlases
Using @SSwarper:
    + this program performs both skullstripping (SS) and NL warping
    + it produces QC images automatically --> no excuse not to check results!!
    + results can be input to afni_proc.py command *very* easily
AFNI's NL alignment performs very well with tools from other software packages
Alignment can be performed on more than just MRI data
    + lots of surgical/clinical applications have CT and other modalities
Alignment can be performed on non-human data
    + @animal_warper does both skullstripping and NL alignment, too (with QC images)
Summary: 
    + use @SSwarper for human studies and @animal_warper for animal studies
    + ALWAYS check your results visually (note the automatic QC in these tools)