#!/bin/tcsh

# ----------------------------------------------------------------------
# Convert a drawn surface ROI to the volume (and back?).
#
# In suma, draw an ROI and save it as (prefix) tuna.lh ,
# then run this script.
#
# This script runs ROI2dataset to convert the tuna ROI into a
# surface dataset (NIML), and then runs 3dSurf2Vol to project
# that into the volume domain, filling the volxels between the
# smooth WM and pial surfaces.
#
# Afterwards, one could view the volume ROI in afni, 'talk' to
# suma, and see how the volume ROI maps back to the surface.
# ----------------------------------------------------------------------

if ( $#argv > 0 ) then
   set prefix = $1
else
   set prefix = tuna
endif

if ( ! -f $prefix.lh.niml.roi ) then
   echo ""
   echo "** missing $prefix.lh.niml.roi : please 'draw' in suma to create it"
   echo "   (save -> $prefix.lh)"
   echo ""
   exit 1
endif

ROI2dataset -prefix $prefix.lh.niml.dset -input $prefix.lh.niml.roi

3dSurf2Vol                                              \
        -spec ../SurfData/SUMA/std.DemoSubj_lh.spec     \
        -surf_A lh.smoothwm.asc                         \
        -surf_B lh.pial.asc                             \
        -sv DemoSubj_SurfVol_Alnd_Exp+orig              \
        -grid_parent DemoSubj_SurfVol_Alnd_Exp+orig     \
        -map_func mode                                  \
        -f_steps 12                                     \
        -sdata $prefix.lh.niml.dset                     \
        -prefix $prefix