vb_fmri_project_Tmap_cortex

 PROJECT VOXEL TMAP ON THE BRAIN SURFACE MODEL

 [Notice]
 spmT_*.img must be coregistered to T1-structural image used for creating
 a brain file

 [Syntax]
  vb_fmri_project_Tmap_cortex(brain_file,act_file,area_file,Tthres,SPMimginfo)

 [Example]
 > brain_file = 'hoge.brain.mat';
 > act_file = 'hoge.act.mat';
 > area_file = 'hoge.area.mat';
 > Tthres    = 5; 
 > Rthres   = 3;
 > SPMimginfo = struct('dirname', '/home/hoge/hoge/spm/',...
 > imgfilenames,{'spmT_0001.img','spmT_0002.img'},imglabels,{'Right index',... 
 > 'Right hand gripping'});
 > vbdot_fmri_project_Tmap_cortex(brain_file,act_file,areafile,Tthres,Rthres,SPMimginfo)

 [Input]
   brain_file : cortical surface model 
   act_file   : act file 
   area_file  : area file
   Tthres     : T-value threshold 
   Rthres     : radius threshold (mm)
   SPMimginfo(ii) : arrays of struct containing information of T-image  
       .dirname : directory name for image file 
       .imgfilename :  file name of image to be projected  
       .imglabel    :  label of image to be projected. These label
                            are used as actkey and areakey.
 
 [Optional]
  loadVmni : if specfied as 1, loading coordinate of brain file as MNI coordinate  

 [Output]
   Acts are added to "act_file" and Areas are added to "area_file"

 2016/07/12 O.Yamashita
 * add loadVmni to input arguments to switch coordinate of brain file 
 2016/07/06 O.Yamashita
 * solve the region expansion problem
 2016/07/01 O.Yamashita
 * first version based on vbdot_fmri_project_Tmap_corext.m

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

0001 function vb_fmri_project_Tmap_cortex(brain_file,act_file,area_file,Tthres,Rthres,SPMimginfo,loadVmni)
0002 % PROJECT VOXEL TMAP ON THE BRAIN SURFACE MODEL
0003 %
0004 % [Notice]
0005 % spmT_*.img must be coregistered to T1-structural image used for creating
0006 % a brain file
0007 %
0008 % [Syntax]
0009 %  vb_fmri_project_Tmap_cortex(brain_file,act_file,area_file,Tthres,SPMimginfo)
0010 %
0011 % [Example]
0012 % > brain_file = 'hoge.brain.mat';
0013 % > act_file = 'hoge.act.mat';
0014 % > area_file = 'hoge.area.mat';
0015 % > Tthres    = 5;
0016 % > Rthres   = 3;
0017 % > SPMimginfo = struct('dirname', '/home/hoge/hoge/spm/',...
0018 % > imgfilenames,{'spmT_0001.img','spmT_0002.img'},imglabels,{'Right index',...
0019 % > 'Right hand gripping'});
0020 % > vbdot_fmri_project_Tmap_cortex(brain_file,act_file,areafile,Tthres,Rthres,SPMimginfo)
0021 %
0022 % [Input]
0023 %   brain_file : cortical surface model
0024 %   act_file   : act file
0025 %   area_file  : area file
0026 %   Tthres     : T-value threshold
0027 %   Rthres     : radius threshold (mm)
0028 %   SPMimginfo(ii) : arrays of struct containing information of T-image
0029 %       .dirname : directory name for image file
0030 %       .imgfilename :  file name of image to be projected
0031 %       .imglabel    :  label of image to be projected. These label
0032 %                            are used as actkey and areakey.
0033 %
0034 % [Optional]
0035 %  loadVmni : if specfied as 1, loading coordinate of brain file as MNI coordinate
0036 %
0037 % [Output]
0038 %   Acts are added to "act_file" and Areas are added to "area_file"
0039 %
0040 % 2016/07/12 O.Yamashita
0041 % * add loadVmni to input arguments to switch coordinate of brain file
0042 % 2016/07/06 O.Yamashita
0043 % * solve the region expansion problem
0044 % 2016/07/01 O.Yamashita
0045 % * first version based on vbdot_fmri_project_Tmap_corext.m
0046 %
0047 % Copyright (C) 2011, ATR All Rights Reserved.
0048 % License : New BSD License(see VBMEG_LICENSE.txt)
0049 
0050 fprintf('============== NOTICE ==========================\n')
0051 fprintf('Please confirm spmT_*.img have been coregistered \n')
0052 fprintf('to the T1-structural image used for creating \n');
0053 fprintf('a brain file.  \n');
0054 fprintf('================================================\n')
0055 
0056 if nargin < 7
0057     loadVmni = 0;
0058 end
0059 
0060 
0061 spmdir = SPMimginfo(1).dirname;
0062 
0063 fprintf('Image directory name : %s,...\n', spmdir);
0064 for jj = 1 : length(SPMimginfo),
0065     fprintf('%s will be registered as %s ...\n', SPMimginfo(jj).imgfilename, SPMimginfo(jj).imglabel);
0066 end
0067 
0068 
0069 for jj = 1 : length(SPMimginfo),
0070     loadimgfile = [spmdir SPMimginfo(jj).imgfilename];
0071     key = SPMimginfo(jj).imglabel;
0072 
0073     % surface mesh
0074     if loadVmni
0075         V = vb_load_cortex(brain_file, 'MNI');
0076     else
0077         V = vb_load_cortex(brain_file, 'subj');
0078     end
0079     V = V * 1000;  % mm
0080       
0081     
0082     % vox image and coordinates
0083     VG=spm_vol(loadimgfile);
0084     [map,XYZ] = spm_read_vols(VG);
0085 
0086     %
0087     % thresholding affects resulting surface image !!!
0088     %
0089       
0090 %     map(map < Tthres) = 0;
0091 %    XYZ = XYZ(:,map~=0);
0092 %    map = map(map ~= 0)';
0093     
0094     ix = find(map~=0);  % brain mask
0095     XYZ = XYZ(:,ix);  
0096     map = map(ix);
0097     map(map < Tthres) = 0; %
0098 
0099   
0100     r2thres = Rthres^2;  % half of diagonal line of cuboid
0101     
0102     
0103     % vox --> surf
0104     Tval = vb_voximg2surimg(XYZ',map(:),V, r2thres, 1);
0105 
0106     
0107    % add act
0108     fprintf('\nAdd T-map to %s with act-key %s \n', act_file, key)
0109     act.xxP = Tval;
0110     act.key = key;
0111     act.spmdir  = spmdir;
0112     act.imgname = SPMimginfo(jj).imgfilename;
0113     vb_add_act(act_file, act, [], OFF);
0114 
0115     % add area
0116     fprintf('Add T-map to %s with area-key %s \n', area_file, key)
0117     area.Iextract = find(Tval~=0);
0118     area.key = key;
0119     area.spmdir  = spmdir;
0120     area.imgname = SPMimginfo(jj).imgfilename;
0121     vb_add_area(area_file, area, [], OFF);
0122     
0123     
0124 end