vb_cortex_normal_variance

 average normal direction in the neighbor of vertex
  [xxdev] = vb_cortex_normal_variance(brainfile,areafile,area_key,...
                                      para, coord_type)
 --- Input
 brainfile
 areafile
 areakey
 coord_type : = 'subj' : subject cortex normal.  [default]
              = 'std'  : standard cortex normal.
 --- Optional input
 para.tan_var : tangential variance coefficient
 para.var_max : tangential variance max

 In the brainfile, 'normal_stat' should be exist:
   normal_stat.neighbor_org : original brain neighbor index list
   normal_stat.normal_org   : original brain normal vector
 --- Output
 xxdev      : deviation from average normal vector  (NP x 3)
 xxdev(:,1) = variance ratio for average normal vector direction
 xxdev(:,2) = variance ratio for tangential direction
 xxdev(:,3) = variance ratio for tangential direction

 angl = Angle between neighboring normal vector and average normal vector

 M. Sato  2006-7-23

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

0001 function   [xxdev ,angl ]= ...
0002              vb_cortex_normal_variance(brainfile,areafile,area_key,...
0003                                        para, coord_type)
0004 % average normal direction in the neighbor of vertex
0005 %  [xxdev] = vb_cortex_normal_variance(brainfile,areafile,area_key,...
0006 %                                      para, coord_type)
0007 % --- Input
0008 % brainfile
0009 % areafile
0010 % areakey
0011 % coord_type : = 'subj' : subject cortex normal.  [default]
0012 %              = 'std'  : standard cortex normal.
0013 % --- Optional input
0014 % para.tan_var : tangential variance coefficient
0015 % para.var_max : tangential variance max
0016 %
0017 % In the brainfile, 'normal_stat' should be exist:
0018 %   normal_stat.neighbor_org : original brain neighbor index list
0019 %   normal_stat.normal_org   : original brain normal vector
0020 % --- Output
0021 % xxdev      : deviation from average normal vector  (NP x 3)
0022 % xxdev(:,1) = variance ratio for average normal vector direction
0023 % xxdev(:,2) = variance ratio for tangential direction
0024 % xxdev(:,3) = variance ratio for tangential direction
0025 %
0026 % angl = Angle between neighboring normal vector and average normal vector
0027 %
0028 % M. Sato  2006-7-23
0029 %
0030 % Copyright (C) 2011, ATR All Rights Reserved.
0031 % License : New BSD License(see VBMEG_LICENSE.txt)
0032 
0033 % tangential variance coefficient
0034 if exist('para','var') & isfield(para,'tan_var')
0035     tan_var = para.tan_var;
0036 else
0037     tan_var = 1;
0038 end
0039 if ~exist('coord_type', 'var')
0040     coord_type = 'subj';
0041 end
0042 
0043 % tangential variance max
0044 if exist('para','var') & isfield(para,'var_max')
0045     var_max = para.var_max;
0046 else
0047     var_max = 2/3;
0048 end
0049 
0050 % tangential angle max
0051 angle_max = pi/2;
0052 
0053 normal_stat = vb_load_normal_statics(brainfile, coord_type);
0054 
0055 %
0056 % --- original vertex near the cortical vertex
0057 %
0058 % normal_stat.neighbor_org : original brain neighbor index list
0059 % normal_stat.normal_org   : original brain normal vector
0060 
0061 %
0062 % --- Angle between neighboring normal vector and average normal vector
0063 %
0064 fprintf('--- Normal vector variance\n')
0065 angl = vb_calc_normal_variance(normal_stat.neighbor_org,normal_stat.normal_org );
0066 
0067 %
0068 % select area
0069 %
0070 if exist('areafile','var') & exist('area_key','var') ...
0071       & ~isempty(areafile) & ~isempty(area_key),
0072     Area = vb_get_area([areafile], area_key);
0073     ix   = Area.Iextract;
0074     angl = angl(ix);
0075 end
0076 
0077 NP    = length(angl);
0078 xxdev = zeros(NP,3);
0079 tvar  = sin( min( tan_var * abs(angl), angle_max) );
0080 tvar  = min( tvar, var_max );
0081 
0082 xxdev(:,1) = 1;
0083 xxdev(:,2) = tvar;
0084 xxdev(:,3) = tvar;
0085 
0086 xxn   = sum(xxdev,2);
0087 xxdev = xxdev./repmat(xxn, [1 3]);