Convert FreeSurfer data to VBMEG format.
- VBMEG Cortical model file(.brain.mat)
- VBMEG Cortical area file(.area.mat)
- VBMEG Cortical act file(.act.mat)
[syntax]
vb_job_brain(brain_parm)
vb_job_brain(proj_root,brain_parm) [old style]
[input]
proj_root : <<string>> VBMEG project root directory.
brain_parm: <<struct>> Parameters for creating cortical surface model
--- fields of brain_parm
analyze_file: <<string>> MRI filename (.nii/.hdr)
brain_parm.FS_left_file = [fs_dir '/bem/lh.smoothwm.asc'];
brain_parm.FS_right_file = [fs_dir '/bem/rh.smoothwm.asc'];
brain_parm.FS_left_infl_file = [fs_dir '/bem/lh.inflated.asc'];
brain_parm.FS_right_infl_file = [fs_dir '/bem/rh.inflated.asc'];
brain_parm.FS_left_curv_file = [fs_dir '/bem/lh.curv.asc'];
brain_parm.FS_right_curv_file = [fs_dir '/bem/rh.curv.asc'];
brain_parm.FS_left_label_file = [fs_dir '/label/lh.cortex.label'];
brain_parm.FS_right_label_file = [fs_dir '/label/rh.cortex.label'];
brain_parm.FS_left_sphere_file = [fs_dir, 'lh.sphere.reg.asc'];
brain_parm.FS_right_sphere_file = [fs_dir, 'rh.sphere.reg.asc'];
brain_parm.FS_sphere_key = 'sphere.reg';
brain_parm.registration_mode='FS'; % FreeSurfer sphere registration.
brain_file : <<string>> Cortical surface model file (.brain.mat).
act_file : <<string>> Cortical activity map file (.act.mat).
area_file : <<string>> Cortical area file (.area.mat).
Nvertex : <<int>> Total number of vertices for cortical surface model
Priority: Nvertex > reduce_ratio
Rmax : <<float>> Maximum radius for neighbor search
N_step : <<int>> Division number of z axis in matching between
cortical surface model and MRI points
display : <<int>> Display progress for this steps
brain_space : <<string>> cortical model map mode.
='mni' : normalize to MNI space
='subj' : individual space
---
[output]
The following files are created:
VBMEG cortical surface model file (.brain.mat)
VBMEG area file (.area.mat)
VBMEG activity map file (.act.mat)
The following variables are stored in .brain.mat file:
Standard brain information.
V : Cortical vertex point cordinate (SPM_Right_m)
F : Patch index structure
xx : Normal vector to cortical surface
xxA : area asigned for each vertex ([m^2])
BV_index : original vertex index in BV/FS corresponding to brain
Vinfo : Vertex dimension structure
xxF{i} : Next-neighbor index for the vertex-i
xxD{i} : Distance between next-neighbor and the vertex-i
xxT{n} : vertex index for n-th triangle
nextIX{i} : Neighbor index list for the vertex-i
nextDD{i} : Distance from the vertex-i
normal_stat
.neighbor_org : BV original brain neighbor for specified vertex
.normal_stat.normal_org : BV original brain normal vector
subj : Individual brain information(structure)
.V : V(n, :) and subj.V(n, :) has same MNI coordinate value.
.F : currently empty(not supported for plotting).
.xx
.xxA
.BV_index
.Vinfo
.nextIX
.nextDD
.normal_stat
The following areas are automatically created and stored in .area.mat
file:
areakey = 'Cortex' : cortex region without corpus area
[history]
Ver.2.0 New version for group analysis
2015-12-27 M. Sato
2017-03-10 M. Sato added some subject elements(subj.xxA, subj.nextIX, subj.nextDD)
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [V,F,xx,BV_index,Vinfo] = ... 0002 vb_job_brain(varargin) 0003 % Convert FreeSurfer data to VBMEG format. 0004 % - VBMEG Cortical model file(.brain.mat) 0005 % - VBMEG Cortical area file(.area.mat) 0006 % - VBMEG Cortical act file(.act.mat) 0007 % 0008 % [syntax] 0009 % vb_job_brain(brain_parm) 0010 % vb_job_brain(proj_root,brain_parm) [old style] 0011 % 0012 % [input] 0013 % proj_root : <<string>> VBMEG project root directory. 0014 % brain_parm: <<struct>> Parameters for creating cortical surface model 0015 % --- fields of brain_parm 0016 % analyze_file: <<string>> MRI filename (.nii/.hdr) 0017 % brain_parm.FS_left_file = [fs_dir '/bem/lh.smoothwm.asc']; 0018 % brain_parm.FS_right_file = [fs_dir '/bem/rh.smoothwm.asc']; 0019 % brain_parm.FS_left_infl_file = [fs_dir '/bem/lh.inflated.asc']; 0020 % brain_parm.FS_right_infl_file = [fs_dir '/bem/rh.inflated.asc']; 0021 % brain_parm.FS_left_curv_file = [fs_dir '/bem/lh.curv.asc']; 0022 % brain_parm.FS_right_curv_file = [fs_dir '/bem/rh.curv.asc']; 0023 % 0024 % brain_parm.FS_left_label_file = [fs_dir '/label/lh.cortex.label']; 0025 % brain_parm.FS_right_label_file = [fs_dir '/label/rh.cortex.label']; 0026 % 0027 % brain_parm.FS_left_sphere_file = [fs_dir, 'lh.sphere.reg.asc']; 0028 % brain_parm.FS_right_sphere_file = [fs_dir, 'rh.sphere.reg.asc']; 0029 % brain_parm.FS_sphere_key = 'sphere.reg'; 0030 % brain_parm.registration_mode='FS'; % FreeSurfer sphere registration. 0031 % 0032 % brain_file : <<string>> Cortical surface model file (.brain.mat). 0033 % act_file : <<string>> Cortical activity map file (.act.mat). 0034 % area_file : <<string>> Cortical area file (.area.mat). 0035 % Nvertex : <<int>> Total number of vertices for cortical surface model 0036 % Priority: Nvertex > reduce_ratio 0037 % Rmax : <<float>> Maximum radius for neighbor search 0038 % N_step : <<int>> Division number of z axis in matching between 0039 % cortical surface model and MRI points 0040 % display : <<int>> Display progress for this steps 0041 % brain_space : <<string>> cortical model map mode. 0042 % ='mni' : normalize to MNI space 0043 % ='subj' : individual space 0044 % --- 0045 % 0046 % [output] 0047 % The following files are created: 0048 % VBMEG cortical surface model file (.brain.mat) 0049 % VBMEG area file (.area.mat) 0050 % VBMEG activity map file (.act.mat) 0051 % 0052 % The following variables are stored in .brain.mat file: 0053 % 0054 % Standard brain information. 0055 % V : Cortical vertex point cordinate (SPM_Right_m) 0056 % F : Patch index structure 0057 % xx : Normal vector to cortical surface 0058 % xxA : area asigned for each vertex ([m^2]) 0059 % 0060 % BV_index : original vertex index in BV/FS corresponding to brain 0061 % Vinfo : Vertex dimension structure 0062 % 0063 % xxF{i} : Next-neighbor index for the vertex-i 0064 % xxD{i} : Distance between next-neighbor and the vertex-i 0065 % xxT{n} : vertex index for n-th triangle 0066 % nextIX{i} : Neighbor index list for the vertex-i 0067 % nextDD{i} : Distance from the vertex-i 0068 % normal_stat 0069 % .neighbor_org : BV original brain neighbor for specified vertex 0070 % .normal_stat.normal_org : BV original brain normal vector 0071 % 0072 % subj : Individual brain information(structure) 0073 % .V : V(n, :) and subj.V(n, :) has same MNI coordinate value. 0074 % .F : currently empty(not supported for plotting). 0075 % .xx 0076 % .xxA 0077 % .BV_index 0078 % .Vinfo 0079 % .nextIX 0080 % .nextDD 0081 % .normal_stat 0082 % 0083 % The following areas are automatically created and stored in .area.mat 0084 % file: 0085 % areakey = 'Cortex' : cortex region without corpus area 0086 % 0087 % [history] 0088 % Ver.2.0 New version for group analysis 0089 % 2015-12-27 M. Sato 0090 % 2017-03-10 M. Sato added some subject elements(subj.xxA, subj.nextIX, subj.nextDD) 0091 % 0092 % Copyright (C) 2011, ATR All Rights Reserved. 0093 % License : New BSD License(see VBMEG_LICENSE.txt) 0094 0095 if length(varargin) == 1 0096 proj_root = []; 0097 brain_parm = varargin{1}; 0098 elseif length(varargin) == 2 0099 proj_root = varargin{1}; 0100 brain_parm = varargin{2}; 0101 end 0102 0103 if ~isfield(brain_parm, 'brain_space') 0104 brain_parm.brain_space = 'mni'; 0105 end 0106 0107 switch(lower(brain_parm.brain_space)) 0108 case 'mni' 0109 vb_disp('Cortex map mode : MNI'); 0110 case 'subj' 0111 % create ver1 format BRAIN-MAT file. 0112 vb_disp('Cortex map mode : Individual'); 0113 vb_job_brain_subj(proj_root, brain_parm); 0114 return; 0115 otherwise 0116 error('Unknown brain_space ''%'' was specified.', brain_parm.brain_space); 0117 end 0118 0119 global vbmeg_inst 0120 const = vb_define_verbose; 0121 VERBOSE_LEVEL_NOTICE = const.VERBOSE_LEVEL_NOTICE; 0122 0123 if ~exist('DEBUG_MODE','var'), DEBUG_MODE = 0; end 0124 0125 % Define constant 0126 define = vbmeg_inst.const; 0127 0128 proj_root = vb_rm_trailing_slash(proj_root); 0129 0130 % 0131 % Do not modify following lines 0132 % 0133 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0134 % 0135 0136 % Output file path 0137 if isempty(proj_root) 0138 brain_file = brain_parm.brain_file; 0139 area_file = brain_parm.area_file; 0140 act_file = brain_parm.act_file; 0141 else 0142 brain_file = fullfile(proj_root, brain_parm.brain_file); 0143 area_file = fullfile(proj_root, brain_parm.area_file); 0144 act_file = fullfile(proj_root, brain_parm.act_file); 0145 end 0146 0147 % ID for MRI image data 0148 analyze_file = brain_parm.analyze_file; 0149 [udir, fname] = vb_get_file_parts(analyze_file); 0150 MRI_ID = vb_mMD5(analyze_file); 0151 0152 %------------------------------------------------------- 0153 % Check registration_mode 0154 %------------------------------------------------------- 0155 flag_spm = (isfield(brain_parm, 'spm_normalization_file') ... 0156 && ~isempty(brain_parm.spm_normalization_file)) ; 0157 0158 flag_fs = (isfield(brain_parm, 'FS_left_sphere_file') ... 0159 && ~isempty(brain_parm.FS_left_sphere_file) ... 0160 && isfield(brain_parm, 'FS_right_sphere_file') ... 0161 && ~isempty(brain_parm.FS_right_sphere_file) ... 0162 && isfield(brain_parm, 'FS_sphere_key') ... 0163 && ~isempty(brain_parm.FS_sphere_key)); 0164 0165 if ~isfield(brain_parm, 'registration_mode') 0166 brain_parm.registration_mode = []; 0167 0168 if flag_fs == 0 && flag_spm == 1, 0169 brain_parm.registration_mode='SPM'; 0170 end 0171 if flag_fs == 1 && flag_spm == 0, 0172 brain_parm.registration_mode='FS'; 0173 end 0174 end 0175 0176 % Reference standard brain 0177 [std_parm, std_brain_dir] = vb_set_icbm152(brain_parm.Nvertex); 0178 std_brain = fullfile(std_brain_dir, std_parm.brain_file); 0179 0180 % List up standard brain resolution 0181 parent_dir = vb_get_file_parts(std_brain_dir); 0182 d = dir(fullfile(parent_dir, '*_*')); 0183 fprintf('Available standard brain model resolution : ') 0184 for k=1:length(d) 0185 if(d(k).isdir == false) 0186 continue; 0187 end 0188 ix = findstr(d(k).name, '_'); 0189 resolution = d(k).name(ix(end)+1:end); 0190 fprintf('%s ', resolution); 0191 if k == length(d), fprintf('\n'); end 0192 end 0193 if exist(std_brain, 'file') ~= 2 0194 % error case 0195 fprintf('Specified resolution(Nvertex=%d) cannot be created.\n', brain_parm.Nvertex); 0196 fprintf('If you use custom resolution, please make new standard brain file as below.\n'); 0197 fprintf('==========\n'); 0198 fprintf('[parm, proj_root] = vb_set_icbm152(%d);\n', brain_parm.Nvertex); 0199 fprintf('make_std_brain_model(proj_root, parm);\n'); 0200 fprintf('==========\n'); 0201 fprintf('Then re-run this function.\n'); 0202 error('Stop processing.'); 0203 end 0204 0205 %------------------------------------------------------- 0206 % Make cortex data from MNI standard brain for group analysis 0207 % 1. Map MNI standard brain to subject brain 0208 % 2. Find nearest point from subject cortical surface 0209 % extracted by FreeSurfer/BV 0210 %------------------------------------------------------- 0211 registration_mode = upper(brain_parm.registration_mode); 0212 switch registration_mode 0213 case 'SPM' 0214 if flag_spm == 0 || flag_fs == 1, 0215 error('Please specify SPM normalization file'); 0216 end; 0217 0218 [V,F,xx,BV_index,Vinfo,Vext,Fext] = vb_make_brain_mni(brain_parm, 'SPM'); 0219 case 'FS' 0220 if flag_fs == 0 || flag_spm == 1, 0221 error('Please specify FS spherical file'); 0222 end; 0223 0224 [V,F,xx,BV_index,Vinfo,Vext,Fext] = vb_make_brain_mni(brain_parm, 'FS'); 0225 otherwise 0226 error('Registration mode error'); 0227 end 0228 0229 if DEBUG_MODE==2, return; end; 0230 %---------------------------------------------- 0231 % Save cortical surface model 0232 %---------------------------------------------- 0233 0234 vb_disp(['Save brain model '], VERBOSE_LEVEL_NOTICE); 0235 vb_disp(sprintf(' filename = %s', brain_file), ... 0236 VERBOSE_LEVEL_NOTICE); 0237 [p, n, e] = vb_get_file_parts(brain_file); 0238 if ~isempty(p) && ~exist(p, 'dir') 0239 vb_mkdir(p); 0240 vb_disp(['Create directory: ' p]); 0241 end 0242 copyfile(std_brain, brain_file); 0243 0244 0245 %---------------------------------------- 0246 % Search next-point index and distance 0247 %---------------------------------------- 0248 vb_disp('Search next-point index and distance ', ... 0249 VERBOSE_LEVEL_NOTICE); 0250 0251 % neighbor index for model vertex (V) 0252 %[xxD, xxF, xxT, xxN] = vb_next_distance( F.F3, V ); % unit : m 0253 %Nzero = length(find( xxN == 0)); 0254 %fprintf('# of No neibor point = %d (# of vertex = %d)', Nzero, length(xxN)) 0255 0256 % neighbor index for extended vertex (Vext) 0257 [xxD, xxF, xxT, xxN] = vb_next_distance( Fext.F3, Vext ); % unit : m 0258 0259 %---------------------------------------------- 0260 % Calculate area assigned to the Vext 0261 %---------------------------------------------- 0262 %tic; 0263 [xxA_all] = vb_calc_patch_area(Vext, Fext.F3, xxT); 0264 %vb_disp(sprintf('%f[sec]',toc), VERBOSE_LEVEL_NOTICE); 0265 0266 if DEBUG_MODE==1, return; end 0267 %---------------------------------------------- 0268 % Search neighbor points along cortex sheet 0269 %---------------------------------------------- 0270 Rmax = brain_parm.R_max; 0271 Display = brain_parm.display; 0272 0273 % total number of vertex 0274 Ndipole = Vinfo.Ndipole; 0275 Vindx = 1:Ndipole; 0276 Vindx_ext = 1:size(Vext,1); 0277 0278 [nextIXext , nextDDext] = ... 0279 vb_find_neighbor_all(Rmax, xxF, xxD, Vindx_ext, Display); 0280 0281 % neighbor index for V 0282 [nextIX, nextDD] = vb_reduce_neighbor_data(Vindx,nextIXext,nextDDext); 0283 0284 % asign external vertex by base vertex according to distance 0285 [ext_index,ext_table] = ... 0286 vb_asign_neighbor_vertex(Vindx,nextIXext,nextDDext); 0287 0288 % asign external vertex area to base vertex area according to distance 0289 xxA = vb_asign_ext_area(xxA_all, Vindx, ext_index, ext_table); 0290 0291 0292 0293 %-------------------------------------------------------------------------- 0294 % Save FS spherical coordinate 0295 %-------------------------------------------------------------------------- 0296 % if flag_fs==1, 0297 % vb_disp(['Save FS spherical coordinate '], VERBOSE_LEVEL_NOTICE); 0298 % 0299 % parm.brain_file = brain_parm.brain_file; 0300 % parm.brain_sphR = brain_parm.FS_right_sphere_file; 0301 % parm.brain_sphL = brain_parm.FS_left_sphere_file; 0302 % parm.key = brain_parm.FS_sphere_key; 0303 % vb_job_brain_add_sphcoord(proj_root, parm); 0304 % end 0305 0306 %-------------------------------------------------------------------------- 0307 % Copy two area files derived from two anatomical divisons 0308 %-------------------------------------------------------------------------- 0309 0310 vb_disp(['Copy area files for Atras'], VERBOSE_LEVEL_NOTICE); 0311 vb_copy_std_atlas_area(brain_file, brain_parm.Nvertex); 0312 0313 %-------------------------------------- 0314 % Make new area and act files 0315 %-------------------------------------- 0316 act_new.key = 'Uniform'; 0317 act_new.xxP = ones(Ndipole,1); 0318 act_new.comment = 'homogeneous fMRI constraint'; 0319 0320 vb_add_act([act_file], act_new, MRI_ID, OFF); 0321 0322 % Make Area file 0323 Vindx = [Vinfo.cortexL; Vinfo.cortexR]; 0324 AreaNew.key = 'Cortex'; 0325 AreaNew.Iextract = Vindx; %[1:Ndipole]'; 0326 0327 vb_add_area(area_file, AreaNew, MRI_ID, OFF); 0328 0329 if DEBUG_MODE==1, return; end; 0330 0331 %--------------------------------------------------- 0332 % Find subject original vertex near the reduced cortical vertex 0333 %--------------------------------------------------- 0334 normal_stat = vb_original_normal_statics(proj_root,brain_parm,BV_index); 0335 0336 % normal average over neighbor points of original brain 0337 xx = vb_calc_normal_average(normal_stat.neighbor_org, normal_stat.normal_org); 0338 0339 vb_disp('Save neighbor statics in the original brain', ... 0340 VERBOSE_LEVEL_NOTICE); 0341 0342 subj = struct; 0343 subj.BV_index = BV_index; 0344 subj.MRI_ID = MRI_ID; 0345 subj.Vinfo = Vinfo; 0346 subj.V = V; 0347 subj.F = []; 0348 subj.xx = xx; 0349 subj.xxA = xxA; 0350 subj.xxD = xxD; 0351 subj.xxF = xxF; 0352 subj.nextIX = nextIX; 0353 subj.nextDD = nextDD; 0354 subj.normal_stat = normal_stat; 0355 vb_save(brain_file, 'subj', 'brain_parm'); 0356 0357 %----------------------------------------- 0358 % Check brain model by 3D & MRI image 0359 %----------------------------------------- 0360 sub_fig = vb_check_brain_model(proj_root,brain_parm,Vext,Fext); 0361 fig_file = strrep(fullfile(proj_root, brain_parm.brain_file),... 0362 '.brain.mat', '.png'); 0363 vb_savefig_as_shown(sub_fig, fig_file); 0364 0365 %-------------------------- 0366 % Save project file 0367 %-------------------------- 0368 proj_file = get_project_filename; 0369 if ~isempty(proj_file) 0370 project_file_mgr('load', proj_file); 0371 project_file_mgr('add', 'brain_parm', brain_parm); 0372 end 0373