#!/bin/tcsh -f

if ("$1" == "-clean") then
   \rm -f lh.OccROIs+orig* 
   \rm -f lh.BigROIs+orig*
   goto END
endif 

if ( ! -f lh.OccROIs.niml.dset || \
     ! -f lh.BigROIs.niml.dset) then
   echo ""
   echo "Missing lh.OccROIs.niml.dset or lh.BigROIs.niml.dset"
   echo "First run:"
   echo "   tcsh run_ROI2dataset"
   echo "then rerun tcsh `basename $0`"
   echo ""
   goto END
endif

#delete output file (from previous run)
if ( ! -f lh.OccROIs+orig.HEAD) then

   #Turn the surface ROIs into volume ROIs
   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_EccExpavir+orig            \
               -map_func      ave                                 \
               -f_steps       10                                  \
               -f_p1_mm -0.5  -f_pn_mm 0.5                        \
               -sdata         lh.OccROIs.niml.dset                \
               -prefix        lh.OccROIs                       
else
   echo "lh.OccROIs+orig.HEAD is already on disk"
endif

#Turn ROI to surf ROI
if ( ! -f lh.BigROIs+orig.HEAD) then

   #Turn the surface ROIs into volume ROIs
   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       20                                  \
               -sdata         lh.BigROIs.niml.dset                \
               -prefix        lh.BigROIs                       
else
   echo "lh.BigROIs+orig.HEAD is already on disk"
endif

#For a more solid ROI, checkout example 1 of SurfPatch -help 

END: