vb_import_fsannot_file

 Import FreeSurfer annotation file. 

 [syntax]
 vb_import_fsannot_file(brain_file,area_file,antl_file,antr_file)

 [input]
 brain_file: <<string>> Cortical surface model file (.brain.mat).
 area_file : <<string>> Cortical area file (.area.mat)
 antl_file : <<string>> FS annotation file for lh.
 antr_file : <<string>> FS annotation file for rh.

 [output]
 Cortical areas are stored into the cortical area file. These areas are
 associated with labels defined with FS. 

 [example]
 >> brain_file = '3D.brain.mat';
 >> area_file  = 'fs_annotation.area.mat';
 >> antl_file  = 'lh.aparc.a2009s.annot';
 >> antr_file  = 'rh.aparc.a2009s.annot';
 >> vb_import_fsannot_file(brain_file,area_file,antl_file,antr_file)

 [history]
 2011-06-17 taku-y
 2012-02-20 taku-y
  [debug] Due to using information in fsannot file without modification,
          color value could be out of range from 0.0 to 1.0. taken
          directly from fsannot file. This bug has been fixed.

0001 function vb_import_fsannot_file(brain_file,area_file,antl_file,antr_file)
0002 % Import FreeSurfer annotation file.
0003 %
0004 % [syntax]
0005 % vb_import_fsannot_file(brain_file,area_file,antl_file,antr_file)
0006 %
0007 % [input]
0008 % brain_file: <<string>> Cortical surface model file (.brain.mat).
0009 % area_file : <<string>> Cortical area file (.area.mat)
0010 % antl_file : <<string>> FS annotation file for lh.
0011 % antr_file : <<string>> FS annotation file for rh.
0012 %
0013 % [output]
0014 % Cortical areas are stored into the cortical area file. These areas are
0015 % associated with labels defined with FS.
0016 %
0017 % [example]
0018 % >> brain_file = '3D.brain.mat';
0019 % >> area_file  = 'fs_annotation.area.mat';
0020 % >> antl_file  = 'lh.aparc.a2009s.annot';
0021 % >> antr_file  = 'rh.aparc.a2009s.annot';
0022 % >> vb_import_fsannot_file(brain_file,area_file,antl_file,antr_file)
0023 %
0024 % [history]
0025 % 2011-06-17 taku-y
0026 % 2012-02-20 taku-y
0027 %  [debug] Due to using information in fsannot file without modification,
0028 %          color value could be out of range from 0.0 to 1.0. taken
0029 %          directly from fsannot file. This bug has been fixed.
0030 
0031 
0032 % load .brain.mat
0033 load(brain_file,'BV_index');
0034 
0035 % load annotation file for lh
0036 [v,l,c] = read_annotation(antl_file);
0037 
0038 % make label data that of VBMEG brain model for lh
0039 [tmp,ix1,ix2] = intersect(BV_index.Left,v+1);
0040 l = l(ix2);
0041 l(ix1) = l;
0042 Ileft0 = length(v);
0043 Ileft = length(BV_index.Left);
0044 
0045 % make area for lh
0046 for i=1:c.numEntries
0047   Area.key = ['lh_' c.struct_names{i}];
0048   Area.Iextract = find(l==c.table(i,5));
0049   Area.clr = c.table(i,1:3);
0050   
0051   % here it is assumed that the maximal color value is 255.
0052   % 2012-02-20 taku-y
0053   Area.clr = (Area.clr)./255;
0054   
0055   vb_add_area(area_file,Area);
0056 end
0057 
0058 % load annotation file for rh
0059 [v,l,c] = read_annotation(antr_file);
0060 
0061 % make label data that of VBMEG brain model for lh
0062 [tmp,ix1,ix2] = intersect(BV_index.Right,v+Ileft0+1);
0063 l = l(ix2);
0064 l(ix1) = l;
0065 
0066 % make area for rh
0067 for i=1:c.numEntries
0068   Area.key = ['rh_' c.struct_names{i}];
0069   Area.Iextract = find(l==c.table(i,5))+Ileft;
0070   Area.clr = c.table(i,1:3);
0071   
0072   % here it is assumed that the maximal color value is 255.
0073   % 2012-02-20 taku-y
0074   Area.clr = (Area.clr)./255;
0075 
0076   vb_add_area(area_file,Area);
0077 end
0078 
0079 return;