# just a quick example for now...
# 
# consider running via:
#
#     tcsh -x s10.surface.analysis |& tee output.s10.surface.analysis

set subj = sb23.blk

# todo:
#
# in spec, needed to set pial parent to SAME
# need to create mid-surface for SurfSmooth command

# just be sure we have the results directory to play in
if ( ! -d $subj.results ) then
    echo missing results directory '$subj.results', exiting...
    exit
endif

cd $subj.results


set runs = (`count -digits 2 1 9`)

# map EPI data to the surface (start with the volreg output)
foreach run ( $runs )
    3dVol2Surf                                          \
        -spec        ../SUMA/sb23_lh_141_std.spec       \
        -sv          ../SUMA/sb23_SurfVol_aligned+orig  \
        -surf_A      smoothwm                           \
        -surf_B      pial                               \
        -grid_parent pb02.$subj.r$run.volreg+orig       \
        -map_func    ave                                \
        -f_steps     20                                 \
        -f_index     nodes                              \
        -out_niml    sb02.$subj.r$run.v2s.niml.dset
end


# blur using SurfSmooth
foreach run ( $runs )
    SurfSmooth                                          \
        -met HEAT_07                                    \
        -spec ../SUMA/sb23_lh_141_std.spec              \
        -surf_A midlayer                                \
        -input sb02.$subj.r$run.v2s.niml.dset           \
        -blurmaster sb02.$subj.r$run.v2s.niml.dset      \
        -output sb03.$subj.r$run.blur.niml.dset         \
        -detrend_in                                     \
        -target_fwhm 5
end

# scale the data, using 3dcalc
# note that no mask is necessary, unless we want to omit low-signal areas
foreach run ( $runs )
    3dTstat -prefix rm.mean_r$run.niml.dset sb03.$subj.r$run.blur.niml.dset
    3dcalc -a sb03.$subj.r$run.blur.niml.dset           \
           -b rm.mean_r$run.niml.dset                   \
           -expr 'min(200, a/b*100)'                    \
           -prefix sb04.$subj.r$run.scale.niml.dset
end

# run the regression analysis
3dDeconvolve -input sb04.$subj.r??.scale.niml.dset                       \
    -polort 2                                                            \
    -num_stimts 15                                                       \
    -stim_times 1 stimuli/blk_times.01.tneg.1D 'BLOCK(30,1)'             \
    -stim_label 1 tneg                                                   \
    -stim_times 2 stimuli/blk_times.02.tpos.1D 'BLOCK(30,1)'             \
    -stim_label 2 tpos                                                   \
    -stim_times 3 stimuli/blk_times.03.tneu.1D 'BLOCK(30,1)'             \
    -stim_label 3 tneu                                                   \
    -stim_times 4 stimuli/blk_times.04.eneg.1D 'BLOCK(30,1)'             \
    -stim_label 4 eneg                                                   \
    -stim_times 5 stimuli/blk_times.05.epos.1D 'BLOCK(30,1)'             \
    -stim_label 5 epos                                                   \
    -stim_times 6 stimuli/blk_times.06.eneu.1D 'BLOCK(30,1)'             \
    -stim_label 6 eneu                                                   \
    -stim_times 7 stimuli/blk_times.07.fneg.1D 'BLOCK(30,1)'             \
    -stim_label 7 fneg                                                   \
    -stim_times 8 stimuli/blk_times.08.fpos.1D 'BLOCK(30,1)'             \
    -stim_label 8 fpos                                                   \
    -stim_times 9 stimuli/blk_times.09.fneu.1D 'BLOCK(30,1)'             \
    -stim_label 9 fneu                                                   \
    -stim_file 10 dfile.rall.1D'[0]' -stim_base 10 -stim_label 10 roll   \
    -stim_file 11 dfile.rall.1D'[1]' -stim_base 11 -stim_label 11 pitch  \
    -stim_file 12 dfile.rall.1D'[2]' -stim_base 12 -stim_label 12 yaw    \
    -stim_file 13 dfile.rall.1D'[3]' -stim_base 13 -stim_label 13 dS     \
    -stim_file 14 dfile.rall.1D'[4]' -stim_base 14 -stim_label 14 dL     \
    -stim_file 15 dfile.rall.1D'[5]' -stim_base 15 -stim_label 15 dP     \
    -gltsym 'SYM: +eneg -fneg'                                           \
    -glt_label 1 eneg_vs_fneg                                            \
    -gltsym 'SYM: 0.5*fneg 0.5*fpos -1.0*fneu'                           \
    -glt_label 2 face_contrast                                           \
    -gltsym 'SYM: tpos epos fpos -tneg -eneg -fneg'                      \
    -glt_label 3 pos_vs_neg                                              \
    -fout -tout -x1D sX.xmat.1D -xjpeg sX.jpg                            \
    -fitts fitts.$subj.niml.dset                                         \
    -bucket stats.$subj.niml.dset