#!/bin/tcsh -f

if ("$1" == "-clean") then
   \rm -f DemoSubj_SurfVol_Alnd_Exp+orig* 
   \rm -f aparc*_Alnd_Exp* 
   \rm -f wm.seg*_Alnd_Exp* 
   \rm -f *ribbon*_Alnd_Exp* 
   goto END
endif 


#Align the anatomical used to create surfaces 
#  to the anatomical aligned with the EPI data
#Also, apply the same transform to segmentation volumes
#12 parameter affine transform is used because DemoSubj_spgrsa+orig
#  had been registered with a 12-parameter transform to the epi data.

if ( ! -f DemoSubj_SurfVol_Alnd_Exp+orig.HEAD) then

@SUMA_AlignToExperiment    -exp_anat DemoSubj_spgrsa+orig.     \
            -surf_anat ../SurfData/SUMA/DemoSubj_SurfVol+orig. \ 
            -align_centers                                     \
            -wd                                                \
            -followers_interp NN                               \
            -surf_anat_followers ../SurfData/SUMA/aparc.a2005s+aseg_rank.nii  \ 
                                 ../SurfData/SUMA/aparc.a2005s+aseg.nii       \ 
                                 ../SurfData/SUMA/lh.ribbon.nii               \ 
                                 ../SurfData/SUMA/rh.ribbon.nii               \
                                 ../SurfData/SUMA/wm.seg.nii

else
   echo "@SUMA_AlignToExperiment has been run already"
endif 
END: