------ Sample scripts for nonlinear warping and using afni_proc.py ------

The files in this directory give you examples of how to run afni_proc.py
with nonlinear spatial warping to MNI space.

FT_anat_fsprep.nii.gz = FT subject T1-weighted anatomical dataset
			-- made isotropic before running FreeSurfer
			   (via check_dset_for_fs.py (see below))
anat_warped     = Directory with results from script s00.warper
                  -- nonlinearly warped anatomical dataset and the
                     warp transformation computed by 3dQwarp
s00.warper      = Script to run @SSwarper to transform the subject's
                    dataset to MNI space and save the warp dataset
                    for later use in afni_proc.py
s05.ap.Awarp    = Script to run afni_proc.py with affine warping
                    to MNI space -- does not need output of s00.warper
s05.ap.Qwarp    = Script to run afni_proc.py with nonlinear warping
                    to MNI space -- requires the output of s00.warper

While running FreeSurfer is not included here, the anatomical input to
@SSwarper was prepared for it via:
	check_dset_for_fs.py                       \
	    -input           FT_anat+orig          \
	    -fix_all                               \
	    -fix_out_prefix  FT_anat_fsprep.nii.gz \
	    -fix_out_vox_dim 1                     \
	    -verb          > check_fs_results.txt

The output from s00.warper is stored in sub-directory anat_warped/
which the script creates. This data is supplied with the AFNI class
data so that you don't have to run this script. If you want to run
the script, you should delete the existing output first:
  \rm -rf anat_warped/
  tcsh s00.warper |& tee s00.warper.out

The analysis scripts can be run with these commands:
  tcsh s05.ap.Awarp |& tee s05.ap.Awarp.out
  tcsh s05.ap.Qwarp |& tee s05.ap.Qwarp.out
The analysis results from these scripts go into sub-directories named
  FT.results.Awarp/  and  FT.results.Qwarp/
The results are not dramatically different - the purpose of using
nonlinear warping is to give better alignment between subjects, and
in this example there is only one subject. The purpose of this
example directory is to show you how to setup analyses that us
nonlinear warping.