---
function vb_make_flat_data(parm)
Incorporate flat map of Brain Voyager. These data are
associated with the brain surface data (.srf) from which
flat map are created. This function needs .brain.mat file,
created based on the brain surface data, to make correspondence
of vertices between the original brain and flat map.
Variables 'IndxL' and 'IndxR' in .brain.mat file are used to make
correspondence, i.e., reduction of vertices from the brain
surface data to VBMEG brain data (.brain.mat).
Input parameters:
parm.[dir/file].brain : VBMEG brain model (.brain.mat)
parm.dir.bvoy_[left/right]: BV flat map directories
parm.file.[left/right]_inf: BV flat map files
parm.[dir/file].inflate : flat model file.
parm.flat_cut_coeff : (Optional) Remove patche if the
maximum length of the side of the
patch is greater than flat_cut_coeff
times the median of maximum length
of all patches.
parm.areafile : (Optional) Area data 'Cortex_flat',
which consists of vertices included
in patches of flat map, is registered
to the area file specified by this
parameter.
2005-02-15 Taku Yoshioka
---
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function vb_make_flat_data(parm) 0002 % --- 0003 % function vb_make_flat_data(parm) 0004 % 0005 % Incorporate flat map of Brain Voyager. These data are 0006 % associated with the brain surface data (.srf) from which 0007 % flat map are created. This function needs .brain.mat file, 0008 % created based on the brain surface data, to make correspondence 0009 % of vertices between the original brain and flat map. 0010 % Variables 'IndxL' and 'IndxR' in .brain.mat file are used to make 0011 % correspondence, i.e., reduction of vertices from the brain 0012 % surface data to VBMEG brain data (.brain.mat). 0013 % 0014 % Input parameters: 0015 % parm.[dir/file].brain : VBMEG brain model (.brain.mat) 0016 % parm.dir.bvoy_[left/right]: BV flat map directories 0017 % parm.file.[left/right]_inf: BV flat map files 0018 % parm.[dir/file].inflate : flat model file. 0019 % parm.flat_cut_coeff : (Optional) Remove patche if the 0020 % maximum length of the side of the 0021 % patch is greater than flat_cut_coeff 0022 % times the median of maximum length 0023 % of all patches. 0024 % parm.areafile : (Optional) Area data 'Cortex_flat', 0025 % which consists of vertices included 0026 % in patches of flat map, is registered 0027 % to the area file specified by this 0028 % parameter. 0029 % 0030 % 2005-02-15 Taku Yoshioka 0031 % --- 0032 % 0033 % Copyright (C) 2011, ATR All Rights Reserved. 0034 % License : New BSD License(see VBMEG_LICENSE.txt) 0035 0036 if ~isfield(parm,'flat_cut_coeff') 0037 parm.flat_cut_coeff = 4; 0038 end 0039 0040 dir = parm.dir ; 0041 file = parm.file; 0042 0043 tic; 0044 fprintf('--- Make Flat model \n'); 0045 0046 % 0047 % --- Brain-Voyager coordinate 0048 % 0049 % V0L/R X:front(0)->back(255), Y:Top(0)->Bottom(255) , Z:left(0)->right(255) 0050 % FOL/R triangle patch 0051 0052 Srf = vb_ScriptLoadSRF([dir.bvoy_left file.left_inf]); 0053 0054 V0L = [Srf.VertexX, Srf.VertexY, Srf.VertexZ]; 0055 F0L = Srf.Triangles+1; 0056 LColor = Srf.MeshColor; 0057 0058 Srf = vb_ScriptLoadSRF([dir.bvoy_right file.right_inf]); 0059 0060 V0R = [Srf.VertexX, Srf.VertexY, Srf.VertexZ]; 0061 F0R = Srf.Triangles+1; 0062 RColor = Srf.MeshColor; 0063 0064 %save([dir.brain 'BVinf-' file.brain], ... 0065 % 'V0L','V0R','F0L','F0R','LColor','RColor'); 0066 0067 clear Srf F0L F0R 0068 0069 % 0070 % x:右(-)->左(+), y:前(-)->後(+), z:下(-)->上(+) 0071 0072 %V2L(:,1) = -V0L(:,3); 0073 V2L(:,1) = V0L(:,1); 0074 V2L(:,2) = V0L(:,3); 0075 V2L(:,3) = -V0L(:,2); 0076 0077 %V2R(:,1) = -V0R(:,3); 0078 V2R(:,1) = -V0R(:,1); 0079 V2R(:,2) = V0R(:,3); 0080 V2R(:,3) = -V0R(:,2); 0081 0082 V2L = V2L./max(abs([V2L(:); V2R(:)])); 0083 V2R = V2R./max(abs([V2L(:); V2R(:)])); 0084 V2L(:,1) = V2L(:,1)+min(V2L(:,1)); 0085 V2R(:,1) = V2R(:,1)-max(V2R(:,1)); 0086 V2L(:,1) = V2L(:,1)+0.1*max(abs([V2L(:,1); V2R(:,1)])); 0087 V2R(:,1) = V2R(:,1)-0.1*max(abs([V2L(:,1); V2R(:,1)])); 0088 0089 % 0090 % --- redeuce patchs 0091 % 0092 %load([dir.brain file.brain], 'F','IndxL','IndxR','MRI_ID','xxA'); 0093 load([dir.brain file.brain],'F','IndxL','IndxR','xxA'); 0094 0095 %if ~strncmp( file.dicom , MRI_ID , 7 ), % compare first 7 character 0096 % fprintf('!! MRI_ID does not match\n'); 0097 % return; 0098 %end; 0099 0100 inf_V3L = V2L(IndxL,:); 0101 inf_V3R = V2R(IndxR,:); 0102 inf_LC = LColor(IndxL,:); 0103 inf_RC = RColor(IndxR,:); 0104 V = [inf_V3L ; inf_V3R]; 0105 inf_C = [inf_LC ; inf_RC ]; 0106 0107 % Calculate patch size 0108 V1L = V(F.F3L(:,1),:); 0109 V2L = V(F.F3L(:,2),:); 0110 V3L = V(F.F3L(:,3),:); 0111 V1R = V(F.F3R(:,1),:); 0112 V2R = V(F.F3R(:,2),:); 0113 V3R = V(F.F3R(:,3),:); 0114 sL = max([sqrt(sum((V2L-V1L).^2,2)) sqrt(sum((V3L-V2L).^2,2)) ... 0115 sqrt(sum((V1L-V3L).^2,2))],[],2); 0116 sR = max([sqrt(sum((V2R-V1R).^2,2)) sqrt(sum((V3R-V2R).^2,2)) ... 0117 sqrt(sum((V1R-V3R).^2,2))],[],2); 0118 %sL = abs(0.5*(sum((V2L-V1L).*(V3L-V1L),2))); 0119 %sR = abs(0.5*(sum((V2R-V1R).*(V3R-V1R),2))); 0120 0121 % Remove large patch 0122 ixL = find(sL < parm.flat_cut_coeff * median([sL; sR])); 0123 ixR = find(sR < parm.flat_cut_coeff * median([sL; sR])); 0124 0125 %ixLv = find(inf_LC<0); 0126 %ixRv = find(inf_RC<0)+length(inf_LC); 0127 %ixL = find(ismember(F.F3L(:,1),ixLv) | ismember(F.F3L(:,2),ixLv) ... 0128 % | ismember(F.F3L(:,3),ixLv)); 0129 %ixR = find(ismember(F.F3R(:,1),ixRv) | ismember(F.F3R(:,2),ixRv) ... 0130 % | ismember(F.F3R(:,3),ixRv)); 0131 %ixL = setxor(1:size(F.F3L,1),ixL); 0132 %ixR = setxor(1:size(F.F3R,1),ixR); 0133 0134 F.F3L = F.F3L(ixL,:); 0135 F.F3R = F.F3R(ixR,:); 0136 F.F3 = [F.F3L; F.F3R]; 0137 0138 % 0139 % --- save the brain model 0140 % 0141 0142 % 拡張子 '.mat' を取り除く 0143 if ~isempty( findstr(file.brain, '.mat') ) 0144 BRAINfile = file.brain(1:findstr(file.brain, '.mat')-1); 0145 else 0146 BRAINfile = file.brain; 0147 end 0148 0149 fprintf(['--- Save flat model (' file.inflate ')\n']); 0150 vb_fsave([dir.inflate file.inflate],'F','V','inf_C','xxA'); 0151 0152 % Register area file 0153 if isfield(parm,'areafile'), 0154 area_new.Iextract = unique(F.F3(:)); 0155 area_new.key = 'Cortex_flat'; 0156 vb_add_area(parm.areafile,area_new); 0157 end 0158