#!/bin/tcsh -f

set subj = '620'

#Align SurfVol to it, and bring along the aseg
if ( ! -f s${subj}_SurfVol_Alnd_Exp+orig.HEAD) then
   echo ""
   echo "Patience while FreeSurfer data are being prepared"
   echo ""
   @SUMA_AlignToExperiment -exp_anat s${subj}_t1_skal2epi+orig. \
                           -surf_anat SUMA/s${subj}_SurfVol+orig. \
                           -align_centers \
                           -followers_interp NN \
                           -surf_anat_followers SUMA/aparc.a2005s+aseg_rank.nii \
                                                SUMA/lh.ribbon.nii     \
                                                SUMA/rh.ribbon.nii     \
                                                SUMA/wm.seg.nii
endif
                                                 
#To view anatomical and parcellation
   @demo_prompt 'Close all AFNI and SUMA sessions.'
   if ($status) goto END
   
   afni -niml -yesplugouts &
   plugout_drive  -com 'SET_PBAR_ALL + 99 1 ROI_256'   \
                  -com 'SET_FUNC_RANGE 256'  \
                  -com "SWITCH_UNDERLAY s${subj}_SurfVol_Alnd_Exp" \
                  -com 'SWITCH_OVERLAY  aparc.a2005s+aseg_rank_Alnd_Exp'   \
                  -com 'SEE_OVERLAY +'   \
                  -com 'OPEN_WINDOW A.axialimage geom=800x400+440+0 mont=4x2:8' \
                  -quit >& /dev/null
   
   @demo_prompt 'Next we will lookup wich area was ranked with 5'
   if ($status) goto END
   echo ""
   echo "To find the label of an area of rank 5"
   echo "use:"
   echo "@FS_roi_label -rankmap SUMA/aparc.a2005s+aseg_rank.rankmap.1D \"
   echo "              -rank 5"
   echo ""
   @FS_roi_label -rankmap SUMA/aparc.a2005s+aseg_rank.rankmap.1D \
                 -rank 5
   
   @demo_prompt 'Next we will lookup integer labels for the putamen'
   if ($status) goto END
   echo ""
   echo "To look for putamen"
   echo "use:"
   echo "@FS_roi_label -rankmap SUMA/aparc.a2005s+aseg_rank.rankmap.1D \"
   echo "              -name putamen"
   echo ""
   @FS_roi_label -rankmap SUMA/aparc.a2005s+aseg_rank.rankmap.1D \
                 -name putamen

#On the surface
   @demo_prompt 'Next we will look at surface-based parcellations'
   if ($status) goto END
   plugout_drive  -com 'SEE_OVERLAY -' \
                  -quit >& /dev/null
                  
   suma  -spec SUMA/s${subj}_both.mini.spec   \
         -sv s${subj}_SurfVol_Alnd_Exp+orig   \
         -niml &
   
   sleep 8
   
   @demo_prompt 'Wait until SUMA is displaying surfaces'
   if ($status) goto END
   #First load the ROIs as a dataset 
   1dcat SUMA/lh.aparc.a2005s.1D.roi'[1]' > SUMA/lh.aparc.1D
   1dcat SUMA/rh.aparc.a2005s.1D.roi'[1]' > SUMA/rh.aparc.1D
   DriveSuma -com surf_cont -label lh.smoothwm.asc  \
                            -load_dset SUMA/lh.aparc.1D   \
                            -view_dset 'n'   
   sleep 3
   DriveSuma -com surf_cont -label rh.smoothwm.asc  \
                            -load_dset SUMA/rh.aparc.1D  \
                            -view_dset 'n'   
                            
   sleep 3 
   DriveSuma -com viewer_cont -key t  \
                              -key 'ctrl+d'  >& /dev/null
      
   echo "Now manually load the parcellation files from SUMA's Draw ROI interface"