Select the dipoles around the active area in fMRI
---- Output
V2ix : Vertex indices corresponding to SPM activity points
P3 : T-value mapped onto cortical surface (normalized so that
maximum=1)
---- Input
spmx3 : SPM point coordinate [x, y, z] (mm)
spmz : t-value
V : 3D coordinate of vertex number n (#Vertex*3)
Originaly written by S.Kajihara
Ver 1.0 modified by M. Sato 2003-3-15
2005-08-30 K. Shibata
* scale of t-value is preserved.
2008-07-23 Taku Yoshioka (Radius check)
2009-05-08 Taku Yoshioka (Radius=0 availale)
2011-06-20 taku-y
[minor] Progress message was added.
---- Parameter setting ----
A vertex point of cortical surface V(n) is chosen as an activity when
it is located inside the sphere of radius 'SPM_Radius' with the center
V(n).
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [V2ix ,P3 ] = vb_spm_to_cortex(spmx3, spmz, V, PARAM) 0002 % Select the dipoles around the active area in fMRI 0003 % 0004 % ---- Output 0005 % V2ix : Vertex indices corresponding to SPM activity points 0006 % P3 : T-value mapped onto cortical surface (normalized so that 0007 % maximum=1) 0008 % ---- Input 0009 % spmx3 : SPM point coordinate [x, y, z] (mm) 0010 % spmz : t-value 0011 % V : 3D coordinate of vertex number n (#Vertex*3) 0012 % 0013 % Originaly written by S.Kajihara 0014 % Ver 1.0 modified by M. Sato 2003-3-15 0015 % 2005-08-30 K. Shibata 0016 % * scale of t-value is preserved. 0017 % 2008-07-23 Taku Yoshioka (Radius check) 0018 % 2009-05-08 Taku Yoshioka (Radius=0 availale) 0019 % 2011-06-20 taku-y 0020 % [minor] Progress message was added. 0021 % 0022 %---- Parameter setting ---- 0023 % A vertex point of cortical surface V(n) is chosen as an activity when 0024 % it is located inside the sphere of radius 'SPM_Radius' with the center 0025 % V(n). 0026 % 0027 % Copyright (C) 2011, ATR All Rights Reserved. 0028 % License : New BSD License(see VBMEG_LICENSE.txt) 0029 0030 SPM_Radius2 = PARAM.SPM_Radius^2 ;% maximum distance for point selection 0031 SPM_zstep = PARAM.SPM_zstep ; % slice step size in z-direction 0032 0033 % Gauss filter parameter to average SPM t-value 0034 Gauss_radius2 = PARAM.Gauss_radius^2;% half-width of Gaussian filter 0035 Gauss_max = PARAM.Gauss_max ; % maximum distance for averaging 0036 Gauss_max2 = PARAM.Gauss_max^2 ; % maximum distance for averaging 0037 0038 % Search range of cortex slices in z-direction 0039 zstep = SPM_zstep; % slice step size in z-direction 0040 zmin = min(V(:,3)) - zstep/2; 0041 zmax = max(V(:,3)) + zstep/2; 0042 spmz = spmz(:); 0043 0044 %---- Parameter setting end---- 0045 V2ix = []; % Index of active dipoles 0046 P3 = []; % Strength of active dipoles 0047 0048 % Loop for slices in z-direction 0049 0050 h = waitbar(0,'Select dipoles'); 0051 prg = 0; 0052 prg_all = zmax-zmin; 0053 vb_disp_nonl(sprintf('%3d %% processed',ceil(100*(prg/prg_all)))); 0054 0055 for zi=zmin:zstep:zmax 0056 % select dipoles on this slices 0057 pixz = find( V(:,3) >= zi & V(:,3) < zi+zstep ); 0058 0059 % select SPM sources near this slice 0060 spix = find(spmx3(:,3) >= zi - Gauss_max ... 0061 & spmx3(:,3) <= zi + Gauss_max + zstep); 0062 0063 % No SPM point or dipole on this slice 0064 if min(size(spix))<1 | min(size(pixz))<1, continue; end 0065 0066 % Find dipoles inside SPM active area 0067 pixy = find(V(pixz,1) >= min(spmx3(spix,1)) - Gauss_max ... 0068 & V(pixz,1) <= max(spmx3(spix,1)) + Gauss_max ... 0069 & V(pixz,2) >= min(spmx3(spix,2)) - Gauss_max ... 0070 & V(pixz,2) <= max(spmx3(spix,2)) + Gauss_max ); 0071 0072 % Find neighboring SPM-voxel for each dipole 0073 0074 0075 % Index for repmat 0076 indxV = 1:3; 0077 indxV = indxV( ones( length(spix), 1 ), : ); 0078 0079 Nnext = size(pixy,1); 0080 spmxd = spmx3(spix,:); 0081 0082 % Loop for candidate dipoles in this slice 0083 for j=1:Nnext, 0084 0085 % Distance between dipole and SPM-voxel 0086 pix = pixz(pixy(j)); % candidate dipole index 0087 Vp = V(pix,:); 0088 d = spmxd - Vp(indxV); 0089 dd = sum(d.^2 , 2 ); 0090 0091 % Radius check (08-07-23 Taku Yoshioka) 0092 if Gauss_max2<SPM_Radius2, Gauss_max2 = SPM_Radius2; end 0093 0094 % index of dipole near SPM-voxel 0095 ix = find( dd <= Gauss_max2 ); % Maximum Averaging radius 0096 ixx = find( dd < SPM_Radius2 ); % Maximum Selection radius 0097 0098 % Check if there are active SPM-voxel in the selection area 0099 if ~isempty( ixx ), 0100 0101 % Add active dipole index 0102 V2ix = [V2ix ; pix]; 0103 0104 % Gauss-averaged SPM strength for the dipole 0105 if Gauss_radius2 > 0, 0106 Pv = sum(spmz(spix(ix)).*exp(-dd(ix)/Gauss_radius2)) ... 0107 /sum(exp(-dd(ix)/Gauss_radius2)); 0108 else 0109 Pv = sum(spmz(spix(ix)))./length(ix); 0110 end 0111 P3 = [P3 ; Pv]; 0112 0113 end 0114 end 0115 0116 waitbar((zi-zmin)/(zmax-zmin)); 0117 for ii=1:15; vb_disp_nonl(sprintf('\b')); end 0118 vb_disp_nonl(sprintf('%3d %% processed',ceil(100*(prg/prg_all)))); 0119 prg = zi-zmin; 0120 end 0121 0122 % Normalization 0123 % P3 = P3./max(P3); 0124 0125 close(h); 0126 drawnow; 0127 vb_disp_nonl(sprintf('\n')); 0128 0129 return;