vb_atlas2vb_aal create an area indices based on the Automated anatomical labeling 'aal'-atlas ---- Syntax vb_atlas2vb_aal(parm) ---- Input fields in 'parm' atlas_dir : Dir of atlas file 'aal.img' save_areafile : Area file saved save_atlasfile : Atlas file saved save_xyzfile : MNI & Talairach coordinate file brainfile : brain file; --- Function required explode : string manupilation ---- NOTE ----- When using the normalize transformation matrix created by 'spm99', back transformation results with a little shift toward X(Left-Right) direction compared with brain file. It is highly recommended to recalculate the transformation matrix by spm2 !!! 2005/03/03 OY 2005/03/28 modified 2005/04/21 second part modified 2005/09/09 ver.030b compatible 2005/12/22 M.Sato 2006/2/3 M.Sato 2006/11/14 M.Sato 2007/03/05 OY * MNI coordinate is stored in brainfile. * save_xyzfile is removed. * A label for 'Corpus' is NaN. 2009-01-05 Taku Yoshioka Supression of confirmation dialog Copyright (C) 2011, ATR All Rights Reserved. License : New BSD License(see VBMEG_LICENSE.txt)
0001 function vb_atlas2vb_aal(parm) 0002 % vb_atlas2vb_aal create an area indices 0003 % based on the Automated anatomical labeling 'aal'-atlas 0004 % ---- Syntax 0005 % vb_atlas2vb_aal(parm) 0006 % 0007 % ---- Input 0008 % fields in 'parm' 0009 % atlas_dir : Dir of atlas file 'aal.img' 0010 % save_areafile : Area file saved 0011 % save_atlasfile : Atlas file saved 0012 % save_xyzfile : MNI & Talairach coordinate file 0013 % brainfile : brain file; 0014 % 0015 % 0016 % --- Function required 0017 % explode : string manupilation 0018 % 0019 % ---- NOTE ----- 0020 % When using the normalize transformation matrix created by 'spm99', 0021 % back transformation results with a little shift 0022 % toward X(Left-Right) direction compared with brain file. 0023 % It is highly recommended to recalculate 0024 % the transformation matrix by spm2 !!! 0025 % 0026 % 2005/03/03 OY 0027 % 2005/03/28 modified 0028 % 2005/04/21 second part modified 0029 % 2005/09/09 ver.030b compatible 0030 % 2005/12/22 M.Sato 0031 % 2006/2/3 M.Sato 0032 % 2006/11/14 M.Sato 0033 % 2007/03/05 OY 0034 % * MNI coordinate is stored in brainfile. 0035 % * save_xyzfile is removed. 0036 % * A label for 'Corpus' is NaN. 0037 % 2009-01-05 Taku Yoshioka 0038 % Supression of confirmation dialog 0039 % 0040 % Copyright (C) 2011, ATR All Rights Reserved. 0041 % License : New BSD License(see VBMEG_LICENSE.txt) 0042 0043 % 0044 % ---- Define aal-atlas 0045 % 0046 0047 % Max value corresponding to Cerebrum cortex region in aal-atlas 0048 % 1-90: Cerebrum, 91-108: Cerebellum, 109-116: Vermis 0049 MaxLabel = 90; 0050 0051 atlas_dir = parm.atlas_dir; 0052 atlas_id = 'aal'; 0053 atlas_text = [atlas_dir 'aal.txt']; 0054 atlas_file = [atlas_dir 'aal.img']; 0055 brainfile = parm.brainfile; 0056 0057 save_areafile = parm.save_areafile; 0058 save_atlasfile = parm.save_atlasfile; 0059 0060 % Max radius to check minimum distance to corresponding point [mm] 0061 if isfield(parm,'Rlimit') 0062 Rlimit = parm.Rlimit; 0063 else 0064 Rlimit = 4; 0065 end 0066 0067 % Max radius to search corresponding point [mm] in the 1st-step 0068 if isfield(parm,'Rmax') 0069 Rmax = parm.Rmax; 0070 else 0071 Rmax = 2; 0072 end 0073 0074 % In the 1st-step, nearest point is searched within Rmax 0075 % In the 2nd-step, nearest point is searched for all candidates 0076 % This value determine, efficiency of search, 0077 % but does not change the result 0078 0079 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0080 %%%%%%%%%%%%%%%%%%%% Don't modify %%%%%%%%%%%%%%%%%%%%%%%%%%% 0081 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0082 0083 %%% Template file is neurological format (right handed spm). 0084 0085 % ----- Corpus label 0086 corpus_key = 'Corpus'; 0087 corpus_label = NaN; 0088 0089 % 0090 % ---- Load MNI-mm-coordinate for subject brain (should be calculated before) 0091 % 0092 load(brainfile, 'Vmni','derr'); 0093 XYZmm = Vmni*1000; % mm 0094 dd = derr*1000; % mm 0095 0096 [Npoint, NdipoleL] = vb_load_cortex_info(brainfile); 0097 Vlabel = zeros(Npoint,1); 0098 dd_label = zeros(Npoint,1); 0099 0100 % 0101 % ----- Remove corpus 0102 % 0103 fprintf('--- Remove corpus region\n'); 0104 [Vindx, Iremove] = vb_remove_corpus_run(brainfile); 0105 Vlabel(Iremove) = corpus_label; 0106 0107 fprintf('# of Corpus points = %d\n',length(Iremove)) 0108 0109 % 0110 % ---- Load Atlas template file 0111 % 0112 0113 % Read image-header 0114 [dim, Trans, XYZmm0] = vb_get_image_info(atlas_file); 0115 0116 % Read atlas-template image 0117 % Z - 3D image data 0118 %Zlabel = read_image(atlas_file); 0119 0120 avw = avw_img_read(atlas_file); 0121 Zlabel = avw.img; 0122 0123 % Zlabel - 3D image data (label value) 0124 % XYZmm0 - 3 x n matrix of XYZ locations 0125 % mm-coordinates in atlas-template (origin is specified by image file) 0126 Zlabel = Zlabel(:); 0127 0128 % Extract labeled region 0129 mni_id = find(Zlabel ~= 0); 0130 Zlabel = Zlabel(mni_id); 0131 XYZmm0 = XYZmm0(:,mni_id)'; 0132 0133 % 0134 % ---- Left brain (Left label is odd integer in 'aal') 0135 % 0136 ix_L = find( mod( Zlabel, 2 ) == 1 & Zlabel < MaxLabel); 0137 ix_LV = Vindx( Vindx <= NdipoleL ); 0138 0139 fprintf('# of Left template points = %d\n',length(ix_L)) 0140 fprintf('# of Left brain points = %d\n',length(ix_LV)) 0141 0142 fprintf('--- Mapping Atlas-label onto 2D cortical surface \n'); 0143 0144 % Find nearest labeled point in atlas 0145 [indx, dd_tmp] = ... 0146 vb_find_nearest_point(XYZmm0(ix_L,:), XYZmm(ix_LV,:), Rmax, 100, 0, 1); 0147 0148 fprintf('# of matched Left brain points = %d\n',length(indx)) 0149 0150 % Find points whose minimum distance to atlas brain region is less than Rlimit 0151 ix_match = find( dd(ix_LV) <= Rlimit & dd_tmp < Rmax & indx > 0 ); 0152 %ix_match = find( dd(ix_LV) <= Rlimit & dd_tmp < Rmax ); 0153 0154 fprintf('# of close points in Left brain = %d\n',length(ix_match)) 0155 0156 % Map label to subject cortex 0157 Vlabel(ix_LV(ix_match)) = Zlabel(ix_L(indx(ix_match))); 0158 dd_label(ix_LV) = dd_tmp; 0159 % 0160 % ---- Right brain (Right label is even integer in 'aal') 0161 % 0162 ix_R = find( mod( Zlabel, 2 ) == 0 & Zlabel <= MaxLabel); 0163 ix_RV = Vindx( Vindx > NdipoleL ); 0164 0165 fprintf('# of Right template points = %d\n',length(ix_R)) 0166 fprintf('# of Right brain points = %d\n',length(ix_RV)) 0167 0168 fprintf('--- Mapping Atlas-label onto 2D cortical surface \n'); 0169 0170 % Find nearest labeled point in atlas 0171 [indx, dd_tmp] = ... 0172 vb_find_nearest_point(XYZmm0(ix_R,:), XYZmm(ix_RV,:), Rmax, 100, 0, 1); 0173 0174 fprintf('# of matched Right brain points = %d\n',length(indx)) 0175 0176 % Find points whose minimum distance to atlas brain region is less than Rlimit 0177 ix_match = find( dd(ix_RV) <= Rlimit & dd_tmp < Rmax & indx > 0 ); 0178 %ix_match = find( dd(ix_RV) <= Rlimit & dd_tmp < Rmax ); 0179 0180 fprintf('# of close points in Right brain = %d\n',length(ix_match)) 0181 0182 % Map label to subject cortex 0183 Vlabel(ix_RV(ix_match)) = Zlabel(ix_R(indx(ix_match))); 0184 dd_label(ix_RV) = dd_tmp; 0185 0186 % Fill label for large distant point 0187 ixz = find( dd_label >= Rmax ); 0188 fprintf('# of unlabeld point = %d\n', length(ixz)) 0189 0190 %fprintf('Filling unlabeled points\n') 0191 %Vlabel = vb_fill_atlas_label(brainfile, Vlabel, ixz, Rlimit); 0192 0193 % 0194 % ---- Save labeled area 0195 % 0196 Nlabel = sum( Vlabel ~= 0 ); % # of labeled points 0197 fprintf('# of all vertex = %d\n',Npoint) 0198 fprintf('# of cortex points = %d\n',length(Vindx)) 0199 fprintf('# of labeled points = %d\n',Nlabel) 0200 0201 % Read atlas text file and extract area keys. 0202 [label, label_name] = vb_read_atlas_label(atlas_text); 0203 0204 % Add Corpus label 0205 Narea = length(label); 0206 label(Narea+1) = corpus_label; 0207 label_name{Narea+1} = corpus_key; 0208 0209 % Intensity of 'Act.xxP' is the label for each vertex 0210 Atlas.key = [atlas_id]; 0211 Atlas.xxP = Vlabel; 0212 Atlas.label = label; 0213 Atlas.label_name = label_name; 0214 Atlas.dd_label = dd_label; 0215 0216 % Save label as actfile 0217 fprintf('Save the atlas file as "%s" \n', save_atlasfile); 0218 vb_add_act(save_atlasfile,Atlas,[],false); 0219 0220 % Save area label into area file 0221 fprintf('Save the area file as "%s" \n', save_areafile); 0222 0223 vb_save_atlas_label(save_areafile,Vlabel,label,label_name); 0224 0225 clear Zlabel Vlabel XYZmm0 XYZmm Zlabel