vb_calc_mni_coord_fs

 Transform coordinate of vertex points on an individual brain to those on the MNI starndard brain. 
 MNI coordinate as well as Talairach coordinate corresponding to 'V' are
 returned. This routine requires FreeSurfer sphere files.
 
 [Usage]
   [XYZmni , XYZtal] = vb_calc_mni_coord_fs(parm);

 [Input]
  Fields in 'parm' struct
            brain_file : Subject Cortical model file(.brain.mat)
  FS_right_sphere_file : Subject FreeSurfer right sphere file(.sphere.reg.asc)
   FS_left_sphere_file : Subject FreeSurfer left  sphere file(.sphere.reg.asc)
         FS_sphere_key : Registration key of sphere coordinate value to brain_file.
 
 [Output]
    XYZmni  : MNI coordinate  (unit:m)       [Nveretex * 3]
    XYZtal  : Talairach coordinate (unit:m)  [Nveretex * 3]

 [History]
   2013-01-25 rhayashi Copy and modified vb_calc_mni_coord.m

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

0001 function [XYZmni, XYZtal] = vb_calc_mni_coord_fs(parm)
0002 % Transform coordinate of vertex points on an individual brain to those on the MNI starndard brain.
0003 % MNI coordinate as well as Talairach coordinate corresponding to 'V' are
0004 % returned. This routine requires FreeSurfer sphere files.
0005 %
0006 % [Usage]
0007 %   [XYZmni , XYZtal] = vb_calc_mni_coord_fs(parm);
0008 %
0009 % [Input]
0010 %  Fields in 'parm' struct
0011 %            brain_file : Subject Cortical model file(.brain.mat)
0012 %  FS_right_sphere_file : Subject FreeSurfer right sphere file(.sphere.reg.asc)
0013 %   FS_left_sphere_file : Subject FreeSurfer left  sphere file(.sphere.reg.asc)
0014 %         FS_sphere_key : Registration key of sphere coordinate value to brain_file.
0015 %
0016 % [Output]
0017 %    XYZmni  : MNI coordinate  (unit:m)       [Nveretex * 3]
0018 %    XYZtal  : Talairach coordinate (unit:m)  [Nveretex * 3]
0019 %
0020 % [History]
0021 %   2013-01-25 rhayashi Copy and modified vb_calc_mni_coord.m
0022 %
0023 % Copyright (C) 2011, ATR All Rights Reserved.
0024 % License : New BSD License(see VBMEG_LICENSE.txt)
0025 
0026 % Cortical model file contains cortex and sphere coordinate
0027 % which is made from ICBM152c Template image.
0028 global vbmeg_inst;
0029 brain_file_template = vbmeg_inst.const.FILE_MNI_ICBM152_BRAIN;
0030 
0031 %
0032 % --- Sphere coregistration between template and subject cortical file
0033 %
0034 [d, f, e] = vb_get_file_parts(parm.brain_file);
0035 proj_root = d;
0036 brain_parm.brain_file = [f, e];
0037 brain_parm.brain_sphR = parm.FS_right_sphere_file;
0038 brain_parm.brain_sphL = parm.FS_left_sphere_file;
0039 brain_parm.key        = parm.FS_sphere_key;
0040 vb_job_brain_add_sphcoord(proj_root, brain_parm);
0041 
0042 % Map template-coordinate to subject cortex
0043 XYZmni = inner_calc_mni_coord(brain_file_template, parm);
0044 
0045 % mni2tal : MNI to Talairach coordinate transformation
0046 XYZtal = mni2tal(XYZmni);
0047 
0048 return;
0049 
0050 function XYZmni = inner_calc_mni_coord(brain_file_template, parm)
0051 % [IN]
0052 %    brain_file_template : template brain file.
0053 %                   parm : same as caller function's.
0054 % [OUT]
0055 %    XYZmni : MNI coordinate
0056 
0057 
0058 % --- load coordinates of cortical models
0059 V1_sph = vb_load_cortex(brain_file_template, 'sphere.reg');
0060 V2_sph = vb_load_cortex(parm.brain_file,     parm.FS_sphere_key);
0061 T_mni  = vb_load_cortex(brain_file_template, 'MNI');
0062 
0063 load(brain_file_template, 'Vinfo');
0064 IL1 = Vinfo.NdipoleL;
0065 load(parm.brain_file,      'Vinfo');
0066 IL2 = Vinfo.NdipoleL;
0067 
0068 V1_sph(1:IL1,1) = V1_sph(1:IL1,1)-400;
0069 V2_sph(1:IL2,1) = V2_sph(1:IL2,1)-400;
0070 
0071 % --- obtain nearest vertex for each of sbj_test vertices
0072 ix = [];
0073 I  = size(V1_sph,1);
0074 
0075 for i=1:size(V2_sph,1)
0076   d         = sum((repmat(V2_sph(i,:),[I 1])-V1_sph).^2,2);
0077   [tmp,ixx] = min(d);
0078   ix        = [ix; ixx];
0079 end
0080 
0081 XYZmni = T_mni(ix,:);
0082 
0083 return;