Make whole brain data (cortex sheet) by reducing BV/FS surface data.
(VBMEG public function)
[syntax]
vb_job_brain_subj(proj_root,brain_parm);
[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_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
(parameters for BrainVoyager cortical surface model) <<string>>
BV_left_file : GM/WM boundary file (.srf) for left hemisphere
BV_right_file : GM/WM boundary file (.srf) for right hemisphere
---
[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:
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
The following areas are automatically created and stored in .area.mat
file:
areakey = 'Cortex' : whole brain
areakey = 'cortex_region' : cortex region without corpus area
areakey = 'corpus_area' : corpus area
[history]
Line 117 was modified by Kawawaki, Dai at 06/04/07
2006/07/21 M. Sato
Make reduced cortex for soft normal constraint
2007/03/05 O. Yamashita
Add lines to compute MNI and Talairach coordinate and two area files
derived from anatomical divisions. These lines are only valid when
spm_normalization_file is specified.
2008-12-24 Taku Yoshioka
Reduce model supression mode
vb_disp() is used for displaying message
Show figures for checking standard brain mask
2010-05-28 Taku Yoshioka
Minor change
2011-01-28 rhayashi
call vb_job_inflate() when brain_parm have fields for inflate model.
2017-03-14 rhayashi
exclude corpus area from 'Cortex'.
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [V,F,xx,BV_index,Vinfo] = vb_job_brain_subj(proj_root,brain_parm, mode) 0002 % Make whole brain data (cortex sheet) by reducing BV/FS surface data. 0003 % (VBMEG public function) 0004 % 0005 % [syntax] 0006 % vb_job_brain_subj(proj_root,brain_parm); 0007 % 0008 % [input] 0009 % proj_root : <<string>> VBMEG project root directory. 0010 % brain_parm: <<struct>> Parameters for creating cortical surface model 0011 % --- fields of brain_parm 0012 % analyze_file: <<string>> MRI filename (.nii/.hdr) 0013 % brain_parm.FS_left_file = [fs_dir '/bem/lh.smoothwm.asc']; 0014 % brain_parm.FS_right_file = [fs_dir '/bem/rh.smoothwm.asc']; 0015 % brain_parm.FS_left_infl_file = [fs_dir '/bem/lh.inflated.asc']; 0016 % brain_parm.FS_right_infl_file = [fs_dir '/bem/rh.inflated.asc']; 0017 % brain_parm.FS_left_curv_file = [fs_dir '/bem/lh.curv.asc']; 0018 % brain_parm.FS_right_curv_file = [fs_dir '/bem/rh.curv.asc']; 0019 % brain_parm.FS_left_label_file = [fs_dir '/label/lh.cortex.label']; 0020 % brain_parm.FS_right_label_file = [fs_dir '/label/rh.cortex.label']; 0021 % 0022 % brain_parm.FS_left_sphere_file = [fs_dir, 'lh.sphere.reg.asc']; 0023 % brain_parm.FS_right_sphere_file = [fs_dir, 'rh.sphere.reg.asc']; 0024 % brain_parm.FS_sphere_key = 'sphere.reg'; 0025 % 0026 % brain_file : <<string>> Cortical surface model file (.brain.mat). 0027 % act_file : <<string>> Cortical activity map file (.act.mat). 0028 % area_file : <<string>> Cortical area file (.area.mat). 0029 % Nvertex : <<int>> Total number of vertices for cortical surface model 0030 % Priority: Nvertex > reduce_ratio 0031 % Rmax : <<float>> Maximum radius for neighbor search 0032 % N_step : <<int>> Division number of z axis in matching between 0033 % cortical surface model and MRI points 0034 % display : <<int>> Display progress for this steps 0035 % 0036 % (parameters for BrainVoyager cortical surface model) <<string>> 0037 % BV_left_file : GM/WM boundary file (.srf) for left hemisphere 0038 % BV_right_file : GM/WM boundary file (.srf) for right hemisphere 0039 % 0040 % --- 0041 % 0042 % [output] 0043 % The following files are created: 0044 % VBMEG cortical surface model file (.brain.mat) 0045 % VBMEG area file (.area.mat) 0046 % VBMEG activity map file (.act.mat) 0047 % 0048 % The following variables are stored in .brain.mat file: 0049 % V : Cortical vertex point cordinate (SPM_Right_m) 0050 % F : Patch index structure 0051 % xx : Normal vector to cortical surface 0052 % xxA : area asigned for each vertex ([m^2]) 0053 % 0054 % BV_index : original vertex index in BV/FS corresponding to brain 0055 % Vinfo : Vertex dimension structure 0056 % 0057 % xxF{i} : Next-neighbor index for the vertex-i 0058 % xxD{i} : Distance between next-neighbor and the vertex-i 0059 % xxT{n} : vertex index for n-th triangle 0060 % nextIX{i} : Neighbor index list for the vertex-i 0061 % nextDD{i} : Distance from the vertex-i 0062 % 0063 % The following areas are automatically created and stored in .area.mat 0064 % file: 0065 % areakey = 'Cortex' : whole brain 0066 % areakey = 'cortex_region' : cortex region without corpus area 0067 % areakey = 'corpus_area' : corpus area 0068 % 0069 % [history] 0070 % Line 117 was modified by Kawawaki, Dai at 06/04/07 0071 % 2006/07/21 M. Sato 0072 % Make reduced cortex for soft normal constraint 0073 % 2007/03/05 O. Yamashita 0074 % Add lines to compute MNI and Talairach coordinate and two area files 0075 % derived from anatomical divisions. These lines are only valid when 0076 % spm_normalization_file is specified. 0077 % 2008-12-24 Taku Yoshioka 0078 % Reduce model supression mode 0079 % vb_disp() is used for displaying message 0080 % Show figures for checking standard brain mask 0081 % 2010-05-28 Taku Yoshioka 0082 % Minor change 0083 % 2011-01-28 rhayashi 0084 % call vb_job_inflate() when brain_parm have fields for inflate model. 0085 % 2017-03-14 rhayashi 0086 % exclude corpus area from 'Cortex'. 0087 % Copyright (C) 2011, ATR All Rights Reserved. 0088 % License : New BSD License(see VBMEG_LICENSE.txt) 0089 0090 const = vb_define_verbose; 0091 VERBOSE_LEVEL_NOTICE = const.VERBOSE_LEVEL_NOTICE; 0092 0093 % Set BV-SPM version (mode = 0 : SBI-compatible) 0094 if ~exist('mode','var'), mode = 1; end; 0095 0096 proj_root = vb_rm_trailing_slash(proj_root); 0097 0098 % 0099 % Do not modify following lines 0100 % 0101 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0102 % 0103 0104 % Output file path 0105 brain_file = [proj_root filesep brain_parm.brain_file]; 0106 area_file = [proj_root filesep brain_parm.area_file ]; 0107 act_file = [proj_root filesep brain_parm.act_file ]; 0108 0109 % ID for MRI image data 0110 [udir, fname] = vb_get_file_parts(brain_parm.analyze_file); 0111 MRI_ID = fname; 0112 0113 %------------------------------------------------------- 0114 % Make cortex coordinate from Brain-Voyager srf-file 0115 %------------------------------------------------------- 0116 switch mode 0117 case 0 0118 % BV-Vox-SPM version (SBI-compatible) 0119 [V,F,xx,BV_index,Vinfo] = vb_make_brain_data(brain_parm); 0120 DEBUG_MODE = 0; 0121 case 1 0122 % BV-SPM version 0123 [V,F,xx,BV_index,Vinfo] = vb_make_brain_data2(brain_parm); 0124 DEBUG_MODE = 0; 0125 case 2 0126 % BV-Vox-SPM version (SBI-compatible) 0127 [V,F,xx,BV_index,Vinfo] = vb_make_brain_data(brain_parm); 0128 DEBUG_MODE = 2; 0129 case 3 0130 % BV-SPM version 0131 [V,F,xx,BV_index,Vinfo] = vb_make_brain_data2(brain_parm); 0132 DEBUG_MODE = 2; 0133 end 0134 0135 if DEBUG_MODE==2, return; end; 0136 0137 %---------------------------------------- 0138 % Search next-point index and distance 0139 %---------------------------------------- 0140 tic; 0141 vb_disp_nonl('Search next-point index and distance ', ... 0142 VERBOSE_LEVEL_NOTICE); 0143 0144 [xxD, xxF, xxT] = vb_next_distance( F.F3, V ); % unit : m 0145 0146 vb_disp(sprintf('%f[sec]',toc), VERBOSE_LEVEL_NOTICE); 0147 0148 % total number of vertex 0149 Ndipole = Vinfo.Ndipole; 0150 Vindx = 1:Ndipole; 0151 0152 %--------------------------------------- 0153 % Smoothing normal vectors (Double mean) 0154 %--------------------------------------- 0155 tic 0156 vb_disp_nonl('Mean of patch normal ', VERBOSE_LEVEL_NOTICE); 0157 0158 % Mean of normal vector for neighboring patch 0159 xx = vb_mean_normal_vector_1(Vindx ,F,V,xx); 0160 % Mean of normal vector for neighbor vertex 0161 xx = vb_mean_normal_vector_4(Vindx ,F,V,xx,xxF); 0162 0163 vb_disp(sprintf('%f[sec]',toc), VERBOSE_LEVEL_NOTICE); 0164 0165 %---------------------------------------------- 0166 % Calculate area assigned to the vertex 0167 %---------------------------------------------- 0168 tic; 0169 [xxA] = vb_calc_patch_area(V, F.F3, xxT); 0170 vb_disp(sprintf('%f[sec]',toc), VERBOSE_LEVEL_NOTICE); 0171 0172 % 0173 % Save cortical surface model 0174 % 0175 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0176 vb_disp(['Save brain model '], VERBOSE_LEVEL_NOTICE); 0177 vb_disp(sprintf(' filename = %s', brain_file), ... 0178 VERBOSE_LEVEL_NOTICE); 0179 vb_save([brain_file],... 0180 'F','V','xx','xxF','xxD','xxA','Vinfo','BV_index','MRI_ID'); 0181 0182 if DEBUG_MODE==1, return; end; 0183 0184 %---------------------------------------------- 0185 % Search neighbor points along cortex sheet 0186 %---------------------------------------------- 0187 Rmax = brain_parm.R_max; 0188 Display = brain_parm.display; 0189 0190 [nextIX , nextDD] = vb_find_neighbor_all(Rmax, xxF, xxD, Vindx, Display); 0191 0192 vb_disp('Save neighbor index of cortical vertex', ... 0193 VERBOSE_LEVEL_NOTICE); 0194 vb_save([brain_file],'nextIX','nextDD'); 0195 0196 %-------------------------------------------------------------------------- 0197 % Calculate MNI coordinate and Talairach coordinate and 0198 % two area files derived from two anatomical divisons (added by OY 07/03/05) 0199 %-------------------------------------------------------------------------- 0200 mni_calculation = ... 0201 (isfield(brain_parm, 'spm_normalization_file') ... 0202 && ~isempty(brain_parm.spm_normalization_file)) ... 0203 ||(isfield(brain_parm, 'FS_left_sphere_file') ... 0204 && ~isempty(brain_parm.FS_left_sphere_file) && ... 0205 isfield(brain_parm, 'FS_right_sphere_file') ... 0206 && ~isempty(brain_parm.FS_right_sphere_file)); 0207 0208 if mni_calculation 0209 atlas_dir = 'MNI_atlas_templates/'; 0210 EXT_brain = '.brain.mat'; 0211 brain_id = brain_file(1:findstr(brain_file,EXT_brain)-1); 0212 0213 %% MNI coordinate 0214 tic 0215 % Computing MNI and Talairach coordinate 0216 vb_job_brain_add_mni_tal_coord(proj_root, brain_parm, false); 0217 0218 %% AAL atlas 0219 tic 0220 mniparm.brainfile = brain_file; 0221 vb_disp_nonl(['Creating an area file consisting of AAL anatomical' ... 0222 'division: '], VERBOSE_LEVEL_NOTICE); 0223 atlas_id = 'aal'; 0224 0225 mniparm.atlas_text = [atlas_dir atlas_id '.txt']; 0226 mniparm.atlas_file = [atlas_dir atlas_id '.img']; 0227 mniparm.atlas_id = atlas_id; 0228 mniparm.atlas_dir = atlas_dir; 0229 0230 0231 mniparm.save_areafile = [brain_id '_' atlas_id '.area.mat']; 0232 mniparm.save_atlasfile = [brain_id '_atlas.act.mat']; % Atlas label 0233 0234 vb_atlas2vb_aal(mniparm) 0235 0236 vb_disp_nonl(sprintf('Done...%f[sec]\n\n',toc)); 0237 0238 0239 %% Brodmann atlas 0240 tic 0241 vb_disp_nonl(['Creating an area file consisting of Brodmann ' ... 0242 'anatomical division: ']); 0243 0244 atlas_id = 'brodmann'; 0245 0246 mniparm.atlas_text = [atlas_dir atlas_id '.txt']; 0247 mniparm.atlas_file = [atlas_dir atlas_id '.img']; 0248 mniparm.atlas_id = atlas_id; 0249 0250 mniparm.save_areafile = [brain_id '_' atlas_id '.area.mat']; 0251 0252 vb_atlas2vb(mniparm) 0253 0254 vb_disp_nonl(sprintf('Done...%f[sec]\n\n',toc), VERBOSE_LEVEL_NOTICE); 0255 else 0256 vb_disp('MNI and Talairach coordinate are not computed.', ... 0257 VERBOSE_LEVEL_NOTICE); 0258 vb_disp(['You can obtain MNI and Talairach coordinate by ' ... 0259 'running vb_atlas2vb.m later '], VERBOSE_LEVEL_NOTICE); 0260 end 0261 0262 %-------------------------------------- 0263 % Make new area and act files 0264 %-------------------------------------- 0265 act_new.key = 'Uniform'; 0266 act_new.xxP = ones(Ndipole,1); 0267 act_new.comment = 'homogeneous fMRI constraint'; 0268 0269 vb_add_act([act_file], act_new, MRI_ID, OFF); 0270 0271 % Make Area file 0272 Vindx = [Vinfo.cortexL; Vinfo.cortexR]; 0273 AreaNew.key = 'Cortex'; 0274 AreaNew.Iextract = Vindx; % rhayashi 2017/3/14 0275 0276 vb_add_area([area_file], AreaNew, MRI_ID, OFF); 0277 0278 %--------------------------------------------------- 0279 % Find original vertex near the cortical vertex 0280 %--------------------------------------------------- 0281 normal_stat = vb_original_normal_statics(proj_root,brain_parm, BV_index); 0282 0283 vb_disp('Save neighbor statics in the original brain', ... 0284 VERBOSE_LEVEL_NOTICE); 0285 vb_save(brain_file,'normal_stat'); 0286 0287 %-------------------------- 0288 % Make reduced cortex 0289 %-------------------------- 0290 if isfield(brain_parm,'make_reduce') & brain_parm.make_reduce, 0291 vb_job_reduced_cortex(proj_root,brain_parm); 0292 end 0293 0294 %-------------------------- 0295 % Import inflate model 0296 %-------------------------- 0297 if has_inflate_model(brain_parm) 0298 vb_job_inflate(proj_root, brain_parm); 0299 end 0300 0301 %----------------------------------------- 0302 % Check brain model by 3D & MRI image 0303 %----------------------------------------- 0304 vb_check_brain_model(proj_root,brain_parm); 0305 0306 %-------------------------- 0307 % Save project file 0308 %-------------------------- 0309 proj_file = get_project_filename; 0310 if ~isempty(proj_file) 0311 project_file_mgr('load', proj_file); 0312 project_file_mgr('add', 'brain_parm', brain_parm, 'vb_job_brain'); 0313 end 0314 0315 % Plot MNI calculation result 0316 % if mni_calculation 0317 % try 0318 % vb_check_mni_coregistration(brain_file); 0319 % catch 0320 % vb_disp(['Failed to plot MNI coordinate value(Out of Memory)', ... 0321 % 'try again: vb_check_mni_coregistration(brain_file)'], .... 0322 % 'WARNING'); 0323 % 0324 % end 0325 % end 0326 0327 return; 0328 0329 function [result] = has_inflate_model(brain_parm) 0330 % Check if brain_parm contains valid fields for inflate model. 0331 % result : return bit pattern 0332 % = 01(1 as int): BV inflate data is set. 0333 % = 10(2 as int): FS inflate data is set. 0334 % = 11(3 as int): Both inflate model were set 0335 result = 0; 0336 BV_BIT = 1; FS_BIT = 2; 0337 % bit all on 0338 result = bitset(result, BV_BIT, 1); 0339 result = bitset(result, FS_BIT, 1); 0340 0341 BV_fields = {'BV_left_infl_file', 'BV_right_infl_file'}; 0342 FS_fields = {'FS_left_infl_file', 'FS_right_infl_file', ... 0343 'FS_left_curv_file', 'FS_right_curv_file'}; 0344 for k=1:length(BV_fields) 0345 if ~isfield(brain_parm, BV_fields{k}) || ... 0346 exist(brain_parm.(BV_fields{k}), 'file') ~= 2 0347 % bit off 0348 result = bitset(result, BV_BIT, 0); 0349 break; 0350 end 0351 end 0352 for k=1:length(FS_fields) 0353 if ~isfield(brain_parm, FS_fields{k}) || ... 0354 exist(brain_parm.(FS_fields{k}), 'file') ~= 2 0355 % bit off 0356 result = bitset(result, FS_BIT, 0); 0357 break; 0358 end 0359 end