Import FreeSurfer annotation file.
[syntax]
vb_import_fsannot_file(brain_file,area_file,antl_file,antr_file)
[input]
brain_file: <<string>> Cortical surface model file (.brain.mat).
atlas_id : <<string>> Cortical area file (.area.mat)
antl_file : <<string>> FS annotation file for lh.
antr_file : <<string>> FS annotation file for rh.
prefix : <<int>> optional
(deafult) = 0 : none is added to the area/act name.
= 1 : lh_/rh_ is added to the area/act name.
[output]
Cortical areas are stored into the cortical area file. These areas are
associated with labels defined with FS.
[example]
>> brain_file = '3D.brain.mat';
>> atlas_id = 'Destrieux';
>> antl_file = 'lh.aparc.a2009s.annot';
>> antr_file = 'rh.aparc.a2009s.annot';
>> vb_import_fsannot_file(brain_file,atlas_id,antl_file,antr_file)
[history]
2011-06-17 taku-y
2012-02-20 taku-y
[debug] Due to using information in fsannot file without modification,
color value could be out of range from 0.0 to 1.0. taken
directly from fsannot file. This bug has been fixed.
2019-10-07 rhayashi
atlas_id is added to make both area file and act file.
2021-3-01 rhayashi
prefix argument is added.0001 function vb_import_fsannot_file(brain_file,atlas_id,antl_file,antr_file, prefix) 0002 % Import FreeSurfer annotation file. 0003 % 0004 % [syntax] 0005 % vb_import_fsannot_file(brain_file,area_file,antl_file,antr_file) 0006 % 0007 % [input] 0008 % brain_file: <<string>> Cortical surface model file (.brain.mat). 0009 % atlas_id : <<string>> Cortical area file (.area.mat) 0010 % antl_file : <<string>> FS annotation file for lh. 0011 % antr_file : <<string>> FS annotation file for rh. 0012 % prefix : <<int>> optional 0013 % (deafult) = 0 : none is added to the area/act name. 0014 % = 1 : lh_/rh_ is added to the area/act name. 0015 % 0016 % [output] 0017 % Cortical areas are stored into the cortical area file. These areas are 0018 % associated with labels defined with FS. 0019 % 0020 % [example] 0021 % >> brain_file = '3D.brain.mat'; 0022 % >> atlas_id = 'Destrieux'; 0023 % >> antl_file = 'lh.aparc.a2009s.annot'; 0024 % >> antr_file = 'rh.aparc.a2009s.annot'; 0025 % >> vb_import_fsannot_file(brain_file,atlas_id,antl_file,antr_file) 0026 % 0027 % [history] 0028 % 2011-06-17 taku-y 0029 % 2012-02-20 taku-y 0030 % [debug] Due to using information in fsannot file without modification, 0031 % color value could be out of range from 0.0 to 1.0. taken 0032 % directly from fsannot file. This bug has been fixed. 0033 % 2019-10-07 rhayashi 0034 % atlas_id is added to make both area file and act file. 0035 % 2021-3-01 rhayashi 0036 % prefix argument is added. 0037 0038 0039 %%%%%%%%%%%%%%%%%%% 0040 % filename prepare 0041 EXT_brain = '.brain.mat'; 0042 brain_id = brain_file(1:findstr(brain_file,EXT_brain)-1); 0043 0044 save_areafile = [brain_id '_' atlas_id '.area.mat']; 0045 save_atlasfile = [brain_id '_' atlas_id '.act.mat']; 0046 0047 if exist(save_atlasfile,'file') 0048 delete(save_atlasfile); 0049 end 0050 if exist(save_areafile,'file') 0051 delete(save_areafile); 0052 end 0053 0054 if ~exist('prefix', 'var') 0055 prefix = 0; 0056 end 0057 if prefix 0058 prefix_l = 'lh_'; 0059 prefix_r = 'rh_'; 0060 else 0061 prefix_l = ''; 0062 prefix_r = ''; 0063 end 0064 0065 %%%%%%%%%%%%%%%%% 0066 % start importing 0067 0068 % load .brain.mat 0069 [Nvertex, tmp2, BV_index, Vinfo] = vb_load_cortex_info(brain_file, 'subj'); 0070 Ncortex = length([Vinfo.cortexL; Vinfo.cortexR]); 0071 0072 % load annotation file for lh 0073 [v,l,c] = read_annotation(antl_file); 0074 0075 % make label data that of VBMEG brain model for lh 0076 [tmp,ix1,ix2] = intersect(BV_index.Left,v+1); 0077 l = l(ix2); 0078 l(ix1) = l; 0079 Ileft0 = length(v); 0080 Ileft = length(BV_index.Left); 0081 0082 % 0083 % make area for lh 0084 % 0085 0086 0087 for i=1:c.numEntries 0088 ix = find(l==c.table(i,5)); 0089 if ~isempty(strfind(c.struct_names{i}, 'FreeSurfer_Defined_Medial_Wall')) || ... 0090 strcmpi(c.struct_names{i}, 'Unknown') || ... 0091 isempty(ix) 0092 continue; 0093 end 0094 Area.key = [prefix_l c.struct_names{i}]; 0095 Area.Iextract = ix; 0096 Area.clr = c.table(i,1:3); 0097 0098 % here it is assumed that the maximal color value is 255. 0099 % 2012-02-20 taku-y 0100 Area.clr = (Area.clr)./255; 0101 0102 vb_add_area(save_areafile,Area); 0103 end 0104 0105 % load annotation file for rh 0106 [v,l,c] = read_annotation(antr_file); 0107 0108 % make label data that of VBMEG brain model for lh 0109 [tmp,ix1,ix2] = intersect(BV_index.Right,v+Ileft0+1); 0110 l = l(ix2); 0111 l(ix1) = l; 0112 0113 % 0114 % make area for rh 0115 % 0116 for i=1:c.numEntries 0117 ix = find(l==c.table(i,5))+Ileft; 0118 if ~isempty(strfind(c.struct_names{i}, 'FreeSurfer_Defined_Medial_Wal')) || ... 0119 strcmpi(c.struct_names{i}, 'Unknown') || ... 0120 isempty(ix) 0121 continue; 0122 end 0123 Area.key = [prefix_r c.struct_names{i}]; 0124 Area.Iextract = ix; 0125 Area.clr = c.table(i,1:3); 0126 0127 % here it is assumed that the maximal color value is 255. 0128 % 2012-02-20 taku-y 0129 Area.clr = (Area.clr)./255; 0130 0131 vb_add_area(save_areafile,Area); 0132 end 0133 0134 % 0135 % make act file(.act.mat) 0136 % 0137 keyset = vb_get_keyset_area(save_areafile); 0138 load(save_areafile,'Area'); 0139 0140 act = struct; 0141 act.key = atlas_id; 0142 act.xxP = zeros(Nvertex, 1); 0143 act.label = 1:length(keyset); 0144 act.label_name = keyset; 0145 for k=1:length(act.label) 0146 act.xxP(Area{k}.Iextract) = act.label(k); % set area number to xxP 0147 end 0148 vb_add_act(save_atlasfile, act, [], false); 0149 0150 fprintf('Save the area file as "%s" \n', save_areafile); 0151 fprintf('Save the act file as "%s" \n', save_atlasfile); 0152 0153 fprintf('# of all vertex = %d\n',Nvertex); 0154 fprintf('# of cortex points = %d\n',Ncortex); 0155 fprintf('# of areas = %d\n',length(keyset)); 0156 0157 0158 0159 return;