Make cortex surface from brain mask image
[V, F, xx, Xcenter] = vb_make_smooth_cortex_surf(subj_mask,analyzefile,Para)
--- Input
analyzefile : Subject analyzefile
subj_mask : Subject brain mask file
Para.gray_val : threshold value for gray matter
if it is empty, only brain mask is used
if is is given, voxel with larger intensity than 'val' is selected
--- バネモデル平滑化パラメタ
Para.Nvertex = 3000; 出力頂点数
Para.Radius = [2 -2]; morphological smoothing
Para.vstep = 1; イメージ処理ボクセルサイズ [mm]
Para.Nloop = 200; マスク境界フィット繰り返し回数
Para.Nlast = 0; バネモデル平滑化繰り返し回数
--- Output
[V, F, xx] : surface vertex, patch index, normal vector
SPM-right-[m] coordinate
Xcenter : Center of cortex to separate left/right (SPM-right-[m])
2007/7/05 Masa-aki Sato
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [V, F, xx, Xcenter] = vb_make_smooth_cortex_surf(subj_mask,analyzefile,Para) 0002 % Make cortex surface from brain mask image 0003 % [V, F, xx, Xcenter] = vb_make_smooth_cortex_surf(subj_mask,analyzefile,Para) 0004 % --- Input 0005 % analyzefile : Subject analyzefile 0006 % subj_mask : Subject brain mask file 0007 % 0008 % Para.gray_val : threshold value for gray matter 0009 % if it is empty, only brain mask is used 0010 % if is is given, voxel with larger intensity than 'val' is selected 0011 % 0012 % --- バネモデル平滑化パラメタ 0013 % Para.Nvertex = 3000; 出力頂点数 0014 % Para.Radius = [2 -2]; morphological smoothing 0015 % Para.vstep = 1; イメージ処理ボクセルサイズ [mm] 0016 % Para.Nloop = 200; マスク境界フィット繰り返し回数 0017 % Para.Nlast = 0; バネモデル平滑化繰り返し回数 0018 % 0019 % --- Output 0020 % [V, F, xx] : surface vertex, patch index, normal vector 0021 % SPM-right-[m] coordinate 0022 % Xcenter : Center of cortex to separate left/right (SPM-right-[m]) 0023 % 0024 % 0025 % 2007/7/05 Masa-aki Sato 0026 % 0027 % Copyright (C) 2011, ATR All Rights Reserved. 0028 % License : New BSD License(see VBMEG_LICENSE.txt) 0029 0030 % --- バネモデル平滑化パラメタ 0031 if ~isfield(Para,'Nvertex'), Para.Nvertex = 3000; end 0032 if ~isfield(Para,'Radius'),Para.Radius = [2 -2];end 0033 if ~isfield(Para,'Nloop'), Para.Nloop = 200; end 0034 if ~isfield(Para,'Nlast'), Para.Nlast = 0; end 0035 if ~isfield(Para,'vstep'), Para.vstep = 1; end; 0036 if ~isfield(Para,'plot_mode'), Para.plot_mode = 0; end 0037 0038 % Gray matter threshold 0039 if isfield(Para,'gray_val'), 0040 val = Para.gray_val; 0041 else 0042 val = []; 0043 end 0044 0045 % Z-slice index for display 0046 zindx = fix([80:15:200]); 0047 0048 if ~isempty(val), 0049 Nbin = 60; 0050 [hst, x] = vb_get_cortex_histogram(subj_mask,analyzefile,Nbin); 0051 stairs(x,hst); hold on 0052 plot([val val],[0 max(hst)],'-r'); 0053 xlim([0 160]) 0054 title('histgram of brain region') 0055 end 0056 % 0057 % --- Get subject cortex mask (voxel size = step [mm]) 0058 % 0059 step = Para.vstep; 0060 0061 if isempty(val) 0062 [avw ,Xcenter] = vb_get_brain_mask(subj_mask,'cortex','', step); 0063 else 0064 [avw ,Xcenter] = vb_get_cortex_mask(subj_mask, analyzefile,'',step,val); 0065 end 0066 0067 % --- Show boundary of mask 0068 if Para.plot_mode==1, 0069 [xyz] = vb_get_boundary(avw.img); 0070 vb_plot_slice( avw.img, xyz, fix(zindx/step), 1, [3, 3], 1); 0071 end 0072 0073 % 0074 % --- Extract smooth surface from mask image [analyze_right_mm] 0075 % 0076 [V, F, xx] = vb_mask_to_surf_expand(avw.img, Para); 0077 0078 % 0079 % --- Plot surface on MRI slice 0080 % 0081 [B, Vdim, Vsize] = vb_load_analyze_to_right(analyzefile); 0082 0083 Vana = vb_analyze_mm_to_analyze(V,Vdim,Vsize); 0084 0085 zindx = fix(zindx/Vsize(3)); 0086 dmax = 10; 0087 xymode=1; 0088 0089 vb_plot_slice_surf(B, Vana, F, zindx, 'z',[3 3],'r-',dmax,xymode); 0090 0091 figure 0092 vb_plot_surf(V,F,[],[],1,1); 0093 view([ -130 10]); 0094 0095 % 0096 % --- SPM-right-[m] coordinate 0097 % 0098 V = vb_analyze_right_mm_to_spm_right(V,Vdim,Vsize); 0099 0100 0101 return 0102 0103 if ~exist('fname','var') | isempty(fname), return; end; 0104 0105 % 0106 % --- Save file 0107 % 0108 fprintf('Save %s \n',fname) 0109 vb_fsave(fname,'V','F','xx','Xcenter') 0110 0111 0112