# --------------------------------
# Align centers of datasets to template
@Align_Centers -base MNI152_T1_2009c+tlrc            \
    -dset anat_mprage_unif+orig                      \
    -child pb02.$subj.r01.tshift+orig.HEAD           \
    pb02.$subj.r02.tshift+orig.HEAD                  \
    pb02.$subj.r03.tshift+orig.HEAD                  \
    pb02.$subj.r04.tshift+orig.HEAD                  \
    pb02.$subj.r05.tshift+orig.HEAD                  \
    pb02.$subj.r06.tshift+orig.HEAD                  \
    pb02.$subj.r07.tshift+orig.HEAD                  \
    pb02.$subj.r08.tshift+orig.HEAD                  \
    pb02.$subj.r09.tshift+orig.HEAD                  \

# --------------------------------
# extract volreg registration base
3dbucket -prefix vr_base pb02.$subj.r01.tshift_shft+orig"[2]"


# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, anat_mprage_ns+orig)
align_epi_anat.py -anat2epi -anat anat_mprage_unif_shft+orig  \
       -suffix _al_keep                             \
	   -epi vr_base+orig -epi_base 0                \
	   -epi_strip 3dAutomask                        \
	   -volreg off -tshift off						\
	   -cost lpc+zz


# ================================== tlrc ==================================
# warp anatomy to standard space
auto_warp.py -base MNI152_T1_2009c+tlrc -input anat_mprage_unif_shft_al_keep+orig \
             -skull_strip_input no -unifize_input no

# move results up out of the awpy directory
# (NL-warped anat, affine warp, NL warp)
# (use typical standard space name for anat)
# (wildcard is a cheap way to go after any .gz)
3dbucket -prefix anat_mprage_unif_shft_al_keep                           \
    awpy/anat_mprage_unif_shft_al_keep.aw.nii*
mv awpy/anat.aff.Xat.1D .
mv awpy/anat.aff.qw_WARP.nii .


# ================================= volreg =================================
# align each dset to base volume
foreach run ( $runs )
    # register each volume to the base
    3dvolreg -verbose -zpad 1 -base vr_base+orig                         \
             -1Dfile dfile.r$run.1D -prefix pb03.$subj.r$run.volreg      \
             -cubic                                                      \
             pb02.$subj.r$run.tshift_shft+orig
end

# make a single file of registration params
cat dfile.r*.1D > dfile_rall.1D

# compute motion magnitude time series: the Euclidean norm
# (sqrt(sum squares)) of the motion parameter derivatives
1d_tool.py -infile dfile_rall.1D -set_nruns 9                            \
           -derivative  -collapse_cols euclidean_norm                    \
           -write motion_${subj}_enorm.1D

# create an anat_final dataset, aligned with stats
3dcopy anat_mprage_unif_shft_al_keep+orig anat_final.$subj

# -----------------------------------------
# warp anat follower datasets (non-liner)
3dNwarpApply -source anat_mprage_unif_shft+orig                              \
             -master anat_final.$subj+orig                               \
             -ainterp wsinc5 -nwarp anat.aff.qw_WARP.nii anat.aff.Xat.1D \
             anat_mprage_unif_shft_al_keep_mat.aff12.1D                      \
             -prefix anat_w_skull_warped