function make_boundaries_main();
% This program was used to generate the label boundaries
% for the paper (http://www.mindboggle.info/papers/):
%
% "Evaluation of 14 nonlinear deformation algorithms 
%  applied to human brain MRI registration" 
%  NeuroImage (2009), doi:10.1016/j.neuroimage.2008.12.037
%  by Arno Klein, Jesper Andersson, Babak A. Ardekani, John Ashburner, 
%     Brian Avants, Ming-Chang Chiang, Gary E. Christensen, D. Louis Collins,
%     James Gee, Pierre Hellier, Joo Hyun Song, Mark Jenkinson, Claude Lepage,
%     Daniel Rueckert, Paul Thompson, Tom Vercauteren, Roger P. Woods, 
%     J. John Mann, and Ramin V. Parsey.
%
% This is the main program for constructing brain label boundaries 
% (calls make_boundaries.m)
%
% Third party code:
% (available from http://www.mathworks.com/matlabcentral/):
% nifti toolbox
%
% (c) 2008, @rno klein
%--------------------------------------------------------------

%---------------------------------------------------
% Setup: load parameters and create output directory
%---------------------------------------------------
 path(path,'/piece-of-mind/registration_study/Programs/nifti');
 more off; format compact; time0 = clock; 
 datapath = '/piece-of-mind/registration_study/';
 
 %reg_method  = 'FLIRT'
 %reg_method  = 'ART'
 %reg_method  = 'ITK'
 %reg_method  = 'AIR'
 %reg_method  = 'ANIMAL' 
 %reg_method  = 'Demons' 
 %reg_method  = 'Fluid'
 %reg_method  = 'FNIRT' 
 reg_method  = 'SyN'
 %reg_method  = 'SPM5_Normalize_direct_8mm' % 183x219x183 -> 182x218x182
 %reg_method  = 'SICLE'  
 %reg_method  = 'Romeo'
 %reg_method  = 'Pasha'
 %reg_method  = 'HAMMER' 
 %reg_method  = 'SPM5_Normalize'
 %reg_method  = 'SPM5_UnifiedSegment'
 %reg_method  = 'SPM5_DARTEL_pairs' 
 
 verbose          = 1;
 save_results     = 1;
 
 singles          = 0;
 pairs            = 1;
 
 if strcmp(reg_method,'SPM5_DARTEL_pairs')==1
      atlas_path  = [datapath 'Atlases/Atlases_MNIspace_RL_DARTELpairseval/'];
 else atlas_path  = [datapath 'Atlases/Atlases_MNIspace/'              ];
 end
 out_path1   = [datapath 'Atlases/Atlases_MNIspace_Borders/'      ]; 
 test_path   = [datapath 'Transformed_Atlases/'     reg_method '/'];
 out_path2   = [datapath 'Evaluations/'             reg_method '/'];
 labels_path = [datapath 'Labels/'                                ];
 
 filestem_tags  = {'g';'m';'l';'c'}; 
 src_filestems3 = {'l1';'l2';'l3';'l4';'l5';'l6';'l7';'l8';'l9';'l10';
                   'l11';'l12';'l13';'l14';'l15';'l16';'l17';'l18';'l19';'l20';
                   'l21';'l22';'l23';'l24';'l25';'l26';'l27';'l28';'l29';'l30';
                   'l31';'l32';'l33';'l34';'l35';'l36';'l37';'l38';'l39';'l40'};
 tgt_filestems3 = src_filestems3;

 for iset = 3
     
   s=sprintf('src_filestems = src_filestems%d;', iset); eval(s);
   s=sprintf('tgt_filestems = tgt_filestems%d;', iset); eval(s);
   s=sprintf('load %s%s_Labels;',labels_path,char(filestem_tags(iset))); eval(s);

 %-----------------------------------------------
 % Loop through sources and targets (and atlases)
 %-----------------------------------------------
   for itarget = 1 : length( tgt_filestems )

     target_name = char(tgt_filestems(itarget));
     
     if singles==1
         
         if verbose > 0
            s=sprintf('disp(''%s'');',target_name); eval(s);
         end

         s=sprintf('TEST = load_nii(''%s'');',[atlas_path target_name '.img']); eval(s);
         TEST = double(TEST.img);

         [Boundaries,Borders] = make_boundaries( TEST, Labels, size(TEST), verbose );

         if save_results==1
            s = ['save ' out_path1 target_name '_borders.mat Borders;']
            eval(s);
         end

     end
     
     if pairs==1

         for isource = 1 : length( src_filestems )

           source_name =  char(src_filestems(isource));                

           %--------------
           % Image volumes
           %--------------
             if verbose > 0
                s=sprintf('disp(''%s_to_%s'');',source_name,target_name); eval(s);
             end

             s=sprintf('TEST = load_nii(''%s'');',[test_path source_name '_to_' target_name '.img']); eval(s);
             TEST = double(TEST.img);

             if strcmp(reg_method,'SPM5_Normalize_direct_8mm')==1
                TEST = TEST(2:end,2:end,2:end);
             end

             [Boundaries,Borders] = make_boundaries( TEST, Labels, size(TEST), verbose );

             if save_results==1
                s = ['save ' out_path2 source_name '_to_' target_name '_borders.mat Borders;'];
                eval(s);
             end
         end
     end
   end
 end

 disp(['Completed in ' num2str(etime(clock,time0)/60) ' minutes']);