Make cortex data from BrainVoyager/FreeSurfer files
[V,F,xx,ORG_index,Vinfo] = vb_make_brain_data(brain_parm)
---
BrainVoyagerまたはFreeSurfer脳データの解像度を下げて全脳データを作る
--- Input
brain_parm : structure with following field
(used for BrainVoyager files)
.BV_left_file : Brain-Voyager left surface file
.BV_right_file : Brain-Voyager right surface file
(used for FreeSurfer files)
.FS_left_file : FreeSurfer left surface file
.FS_right_file : FreeSurfer right surface file
.FS_xfm_file : Talairach transformation file
.analyze_file : MRI analyze file
.reduce_ratio : ratio of reducing vertex points
BV皮質モデルからVBMEG脳モデルを作成するときの頂点数の削減率
.N_step : Division number in searching match points
頂点対応探索時のZ軸方向分割数
--- Output
V : Cortical vertex point cordinate (SPM_Right_m) [Nvertex, 3]
頂点位置 （ 頂点の数, 3）
xx : Normal vector to cortical surface [Nvertex, 3]
頂点の法線方向と位置（ 頂点の数, 3）
F : Patch index structure
面(3角形)を構成する３つの頂点番号 ( 面の数, 3)
.F3R : Right cortex
.F3L : Left cortex
.F3 : Left + Right
BV_index : original vertex index in BV corresponding to brain
.Left : Left brain
.Right : Right brain
Vinfo : Vertex dimension structure
.Ndipole : # of vertex
.NdipoleL : # of vertex in Left cortex
.Npatch : # of patch
.Coord = 'SPM_Right_m';
Originaly written by S.Kajihara
Ver 1.1 modified by M. Sato 2003-4-15
Modified by Taku Yoshioka
2003-07-11
・ファイルに保存するデータ構造を変更
・メッセージを少し変更
2003-07-29
・座標変換時のオフセットを切替えられるように変更
2003-10-08
・MRI-Voxel座標データを保存(元の仕様)
2005-03-20 Modified by TY
Ver 2.0 modified by M. Sato 2005-4-8
座標系をSPM右手座標に変換する
Analyze ファイルが必要
(DICOM イメージファイルは不要)
modified by M. Sato 2005-8-1
Vinfo 追加
modified by M. Sato 2005-8-9
パラメタと変数名の大幅見直し変更
2008-10-16 Taku Yoshioka
Non-XFM file support for FreeSurfer ver. 4.0
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [V,F,xx,BV_index,Vinfo] = vb_make_brain_data(brain_parm); 0002 % Make cortex data from BrainVoyager/FreeSurfer files 0003 % [V,F,xx,ORG_index,Vinfo] = vb_make_brain_data(brain_parm) 0004 % 0005 % --- 0006 % BrainVoyagerまたはFreeSurfer脳データの解像度を下げて全脳データを作る 0007 % 0008 %--- Input 0009 % 0010 % brain_parm : structure with following field 0011 % (used for BrainVoyager files) 0012 % .BV_left_file : Brain-Voyager left surface file 0013 % .BV_right_file : Brain-Voyager right surface file 0014 % 0015 % (used for FreeSurfer files) 0016 % .FS_left_file : FreeSurfer left surface file 0017 % .FS_right_file : FreeSurfer right surface file 0018 % .FS_xfm_file : Talairach transformation file 0019 % 0020 % .analyze_file : MRI analyze file 0021 % .reduce_ratio : ratio of reducing vertex points 0022 % BV皮質モデルからVBMEG脳モデルを作成するときの頂点数の削減率 0023 % .N_step : Division number in searching match points 0024 % 頂点対応探索時のZ軸方向分割数 0025 % 0026 %--- Output 0027 % 0028 % V : Cortical vertex point cordinate (SPM_Right_m) [Nvertex, 3] 0029 % 頂点位置 （ 頂点の数, 3） 0030 % xx : Normal vector to cortical surface [Nvertex, 3] 0031 % 頂点の法線方向と位置（ 頂点の数, 3） 0032 % F : Patch index structure 0033 % 面(3角形)を構成する３つの頂点番号 ( 面の数, 3) 0034 % .F3R : Right cortex 0035 % .F3L : Left cortex 0036 % .F3 : Left + Right 0037 % BV_index : original vertex index in BV corresponding to brain 0038 % .Left : Left brain 0039 % .Right : Right brain 0040 % Vinfo : Vertex dimension structure 0041 % .Ndipole : # of vertex 0042 % .NdipoleL : # of vertex in Left cortex 0043 % .Npatch : # of patch 0044 % .Coord = 'SPM_Right_m'; 0045 % 0046 % Originaly written by S.Kajihara 0047 % Ver 1.1 modified by M. Sato 2003-4-15 0048 % 0049 % Modified by Taku Yoshioka 0050 % 2003-07-11 0051 % ・ファイルに保存するデータ構造を変更 0052 % ・メッセージを少し変更 0053 % 2003-07-29 0054 % ・座標変換時のオフセットを切替えられるように変更 0055 % 2003-10-08 0056 % ・MRI-Voxel座標データを保存(元の仕様) 0057 % 0058 % 0059 % 2005-03-20 Modified by TY 0060 % 0061 % Ver 2.0 modified by M. Sato 2005-4-8 0062 % 座標系をSPM右手座標に変換する 0063 % Analyze ファイルが必要 0064 % (DICOM イメージファイルは不要) 0065 % 0066 % modified by M. Sato 2005-8-1 0067 % Vinfo 追加 0068 % modified by M. Sato 2005-8-9 0069 % パラメタと変数名の大幅見直し変更 0070 % 2008-10-16 Taku Yoshioka 0071 % Non-XFM file support for FreeSurfer ver. 4.0 0072 % 0073 % Copyright (C) 2011, ATR All Rights Reserved. 0074 % License : New BSD License(see VBMEG_LICENSE.txt) 0075 0076 error('This function is a canditate to be removed, but invoked.'); 0077 0078 global vbmeg_inst; 0079 define = vbmeg_inst.const; 0080 0081 % Define constant 0082 TRANS_COORDINATE = 0; 0083 TRANS_NORMAL = 1; 0084 0085 % V0L/R Brain-Voyager coordinate 0086 % n0L/R inward-normal unit vector 0087 % FOL/R triangle patch 0088 tic; 0089 if isfield(brain_parm,'BV_left_file') & ... 0090 ~isempty(brain_parm.BV_left_file), 0091 % 0092 % --- Brain-Voyager coordinate 0093 % 0094 % [Left-hand coordinate] 0095 % X:Front(0) -> Back(255) 0096 % Y:Top(0) -> Bottom(255) 0097 % Z:Right(0) -> Left(255) 0098 fprintf('\n--- Make brain model using BrainVoyager SRF files '); 0099 filetype = 'BrainVoyager'; 0100 0101 Srf = vb_ScriptLoadSRF(brain_parm.BV_left_file); 0102 V0L = [Srf.VertexX, Srf.VertexY, Srf.VertexZ]; 0103 n0L = [Srf.NormalX, Srf.NormalY, Srf.NormalZ]; 0104 F0L = Srf.Triangles+1; 0105 0106 Srf = vb_ScriptLoadSRF(brain_parm.BV_right_file); 0107 V0R = [Srf.VertexX, Srf.VertexY, Srf.VertexZ]; 0108 n0R = [Srf.NormalX, Srf.NormalY, Srf.NormalZ]; 0109 F0R = Srf.Triangles+1; 0110 elseif isfield(brain_parm,'FS_left_file') & ... 0111 ~isempty(brain_parm.FS_left_file), 0112 fprintf('\n--- Make brain model using FreeSurfer .asc files '); 0113 filetype = 'FreeSurfer'; 0114 0115 [V0L,F0L] = vb_fs_load_surface(brain_parm.FS_left_file,... 0116 brain_parm.FS_xfm_file,1.0); 0117 [V0R,F0R] = vb_fs_load_surface(brain_parm.FS_right_file,... 0118 brain_parm.FS_xfm_file,1.0); 0119 0120 [tmp1,tmp2,n0L] = vb_out_normal(F0L,V0L); 0121 [tmp3,tmp4,n0R] = vb_out_normal(F0R,V0R); 0122 n0L = -1*n0L; 0123 n0R = -1*n0R; 0124 0125 if size(tmp1,1)~=size(F0L,1) | size(tmp2,1)~=size(V0L,1) | ... 0126 size(tmp3,1)~=size(F0R,1) | size(tmp4,1)~=size(V0R,1), 0127 error(['There are some isolated pathces in the FreeSurfer ' ... 0128 'cortical model.']); 0129 end 0130 end 0131 fprintf('%f[sec]\n',toc); 0132 0133 switch filetype 0134 case 'BrainVoyager', 0135 % 0136 % --- MRI-Voxel coordinate 0137 % 0138 % [Right-hand coordinate] 0139 % X:Front(1) -> Back(256) 0140 % Y:Top(1) -> Bottom(256) 0141 % Z:Left(1) -> Right(191) 0142 % 0143 tic; 0144 fprintf('--- Coordinate transformation (BV to VOX) '); 0145 0146 [Vdim, Vsize] = analyze_hdr_read(brain_parm.analyze_file); 0147 0148 V2L = vb_bvoyger_to_vox(V0L,Vdim,Vsize,TRANS_COORDINATE); 0149 V2R = vb_bvoyger_to_vox(V0R,Vdim,Vsize,TRANS_COORDINATE); 0150 0151 n2L = vb_bvoyger_to_vox(n0L,Vdim,Vsize,TRANS_NORMAL); 0152 n2R = vb_bvoyger_to_vox(n0R,Vdim,Vsize,TRANS_NORMAL); 0153 0154 fprintf('%f[sec]\n',toc); 0155 case 'FreeSurfer' 0156 V2L = V0L; 0157 V2R = V0R; 0158 n2L = n0L; 0159 n2R = n0R; 0160 end 0161 0162 % 0163 % --- Redeuce patchs 0164 % 0165 tic; 0166 fprintf('--- Reduce cortical vertices '); 0167 0168 [F3L,V3L] = vb_reducepatch( F0L, V2L, brain_parm.reduce_ratio ); 0169 [F3R,V3R] = vb_reducepatch( F0R, V2R, brain_parm.reduce_ratio ); 0170 0171 fprintf('%f[sec]\n',toc); 0172 0173 % 0174 % --- Find original vertex point in BV-model corresponding to reduced model 0175 % 0176 tic; 0177 fprintf('--- Find original point corresponding to reduced model '); 0178 0179 IndxL = vb_find_match_point( V2L, V3L, brain_parm.N_step ); 0180 IndxR = vb_find_match_point( V2R, V3R, brain_parm.N_step ); 0181 0182 fprintf('%f[sec]\n',toc); 0183 0184 % --- Normal vector obtained from original BV-model 0185 n3L = n2L(IndxL,:); 0186 n3R = n2R(IndxR,:); 0187 0188 % 0189 % --- Right-hand SPM coordinate [mm] 0190 % 0191 % [Right-hand coordinate] 0192 % X: Left(-191/2) -> Right(191/2) 0193 % Y: Back(-256/2) -> Front(256/2) 0194 % Z: Bottom(-256/2) -> Top(256/2) 0195 % 0196 switch filetype, 0197 case 'BrainVoyager', 0198 tic; 0199 fprintf('--- Coordinate transformation (VOX to SPM-ANALYZE) '); 0200 V3L = vb_vox_to_spm_right(V3L,Vdim,Vsize,TRANS_COORDINATE); 0201 V3R = vb_vox_to_spm_right(V3R,Vdim,Vsize,TRANS_COORDINATE); 0202 0203 n3L = vb_vox_to_spm_right(n3L,Vdim,Vsize,TRANS_NORMAL); 0204 n3R = vb_vox_to_spm_right(n3R,Vdim,Vsize,TRANS_NORMAL); 0205 0206 fprintf('%f[sec]\n',toc); 0207 case 'FreeSurfer', 0208 end 0209 0210 % Vertex number of reduced model 0211 NdipoleL = size(V3L,1); 0212 NdipoleR = size(V3R,1); 0213 Ndipole = NdipoleL + NdipoleR; 0214 0215 F3R = F3R + NdipoleL; 0216 F3 = [F3L ; F3R]; 0217 n3 = [n3L ; n3R]; 0218 0219 NdipoleL0 = size(V0L,1); 0220 clear V0L V0R V2L V2R F0L F0R n0L n0R n2L n2R Srf 0221 0222 % 0223 % --- SPM cordinate in [m] , Normal vector is outward. 0224 % 0225 tic; 0226 fprintf('--- Change coordinate to [m] '); 0227 V = [V3L ; V3R]./1000; 0228 0229 % Normalize normal vectors 0230 nn = sqrt(sum(n3.^2 ,2)); 0231 ix = find(nn<eps); 0232 if ~isempty(ix), 0233 fprintf('!! There are abnormal normal vector \n'); 0234 nn(ix) = 1; 0235 end 0236 xx = -n3./repmat(nn ,[1 3]); 0237 0238 0239 % triangle patch index for left/right brain 0240 Npatch = size(F3,1); 0241 F.F3 = F3; 0242 F.F3R = F3R; 0243 F.F3L = F3L; 0244 F.NdipoleL = NdipoleL; 0245 0246 % BrainVoyager vertex index corresponding to reduced brain 'V' 0247 BV_index.Left = IndxL; 0248 BV_index.Right = IndxR+NdipoleL0; 0249 0250 % Dimensional info 0251 Vinfo.Ndipole = Ndipole; 0252 Vinfo.NdipoleL = NdipoleL; 0253 Vinfo.Npatch = Npatch; 0254 Vinfo.NdipoleL0 = NdipoleL0; 0255 Vinfo.Coord = 'SPM_Right_m'; 0256 0257 clear V3L V3R n3L n3R 0258 0259 fprintf('%f[sec]\n',toc); 0260