load cortex vertex coordinate from brain file
-- Syntax
[Vout,F,xx,inf_C,xxA] = vb_load_cortex(brainfile,coord_type,analyzefile)
-- Input
brainfile : <required>Brain file name
:
coord_type : <optional> <<string>> ID of coordinate. case-insensitive.
: [not be specified]
: (default) return V of brainfile as 'Vout'
: 'SPM_Right_m' [m]
: 'Analyze_Right_voxel' [voxel]
: 'Inflate'
: 'Talairach': Talairach coordinate [mm]
: 'MNI' : MNI-space coordinate [mm]
: 'subj' : return subject cortex.
: If coord_type does not match with the all of above IDs,
it is interpreted as a user-specified ID and searching
struct variable 'Vall', if any.
:
analyzefile : <conditional required> corresponding to brainfile
: If the data is old format, or 'Analyze_Right_voxel' or
: 'SPM_Right_m' is requested, analyzefile is needed.
--- Output
Vout : cortex vertex coordinate [Nvertex, 3]
F : Triangle patch index structure
xx : Normal vector to cortical surface [Nvertex, 3]
inf_C : Color corresponding to Gyrus in inflate data [Nvertex, 1]
xxA : patch area assigned to each vertex [Nvertex, 1]
written by M. Sato 2005-8-1
Modified by Taku Yoshioka 2005-08-22
2007-03-12 (Sako) added two coord_types ('Talairach' and 'MNI')
2007-8-6 Masa-aki Sato bug fix for old format
2008-1-16 Masa-aki Sato 'V' is returned if there is no inflate data
2010-11-18 Taku Yoshioka
User-specified coordinate type supported.
Message display changed (vb_disp).
2017-1-25 rhayashi Added coord_type 'subj'
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [Vout,F,xx,inf_C,xxA]= vb_load_cortex(brainfile, coord_type, analyzefile) 0002 % load cortex vertex coordinate from brain file 0003 % 0004 % -- Syntax 0005 % [Vout,F,xx,inf_C,xxA] = vb_load_cortex(brainfile,coord_type,analyzefile) 0006 % 0007 % -- Input 0008 % brainfile : <required>Brain file name 0009 % : 0010 % coord_type : <optional> <<string>> ID of coordinate. case-insensitive. 0011 % : [not be specified] 0012 % : (default) return V of brainfile as 'Vout' 0013 % : 'SPM_Right_m' [m] 0014 % : 'Analyze_Right_voxel' [voxel] 0015 % : 'Inflate' 0016 % : 'Talairach': Talairach coordinate [mm] 0017 % : 'MNI' : MNI-space coordinate [mm] 0018 % : 'subj' : return subject cortex. 0019 % : If coord_type does not match with the all of above IDs, 0020 % it is interpreted as a user-specified ID and searching 0021 % struct variable 'Vall', if any. 0022 % : 0023 % analyzefile : <conditional required> corresponding to brainfile 0024 % : If the data is old format, or 'Analyze_Right_voxel' or 0025 % : 'SPM_Right_m' is requested, analyzefile is needed. 0026 % 0027 % --- Output 0028 % Vout : cortex vertex coordinate [Nvertex, 3] 0029 % F : Triangle patch index structure 0030 % xx : Normal vector to cortical surface [Nvertex, 3] 0031 % inf_C : Color corresponding to Gyrus in inflate data [Nvertex, 1] 0032 % xxA : patch area assigned to each vertex [Nvertex, 1] 0033 % 0034 % written by M. Sato 2005-8-1 0035 % Modified by Taku Yoshioka 2005-08-22 0036 % 2007-03-12 (Sako) added two coord_types ('Talairach' and 'MNI') 0037 % 2007-8-6 Masa-aki Sato bug fix for old format 0038 % 2008-1-16 Masa-aki Sato 'V' is returned if there is no inflate data 0039 % 2010-11-18 Taku Yoshioka 0040 % User-specified coordinate type supported. 0041 % Message display changed (vb_disp). 0042 % 2017-1-25 rhayashi Added coord_type 'subj' 0043 % Copyright (C) 2011, ATR All Rights Reserved. 0044 % License : New BSD License(see VBMEG_LICENSE.txt) 0045 0046 inf_C = []; 0047 0048 % --- check brain file --- % 0049 if ~exist('brainfile', 'var'), brainfile = []; end; 0050 [brain_id] = inner_check_brainfile(brainfile); 0051 0052 % --- MAIN PROCEDURE --------------------------------------------------------- % 0053 % 0054 0055 % --- DEFAULT 0056 % 0057 if ~exist('coord_type','var'), 0058 load(brainfile,'V','F','xx','xxA'); 0059 Vout = V; 0060 return; 0061 end; 0062 0063 load(brainfile,'V*','F','xx','xxA'); 0064 0065 switch lower(coord_type) 0066 % --- Inflate 0067 % 0068 case 'inflate' 0069 if exist('Vinflate','var') 0070 Vout = Vinflate; 0071 load(brainfile,'inf_C'); 0072 else 0073 inflated_brainfile = [brain_id '.inflate.mat']; 0074 if exist(inflated_brainfile, 'file') 0075 load(inflated_brainfile, 'V','inf_C') 0076 Vout = V; 0077 else 0078 Vout = V; 0079 inf_C = ones(size(V,1),1); 0080 vb_disp(['There is no inflate brain data:' brainfile ]); 0081 end; 0082 end; 0083 0084 % --- SPM_Right_m 0085 % 0086 case 'spm_right_m' 0087 if exist('Vinfo','var') 0088 Vout = V; 0089 else 0090 vb_disp('Old SBI brain file '); 0091 [Vdim, Vsize] = analyze_hdr_read(analyzefile); 0092 Vout = vb_vox_to_spm_right(Vox,Vdim,Vsize)*0.001;% mm -> m 0093 end; 0094 0095 % --- Analyze_Right_voxel 0096 % 0097 case 'analyze_right_voxel' 0098 if exist('Vinfo','var') 0099 if exist('Vox','var') 0100 Vout = Vox; 0101 else 0102 [Vdim, Vsize] = analyze_hdr_read(analyzefile); 0103 Vout = vb_spm_right_to_analyze_right(V,Vdim,Vsize); 0104 end; 0105 else 0106 vb_disp('Old SBI brain file '); 0107 [Vdim, Vsize] = analyze_hdr_read(analyzefile); 0108 Vout = vb_vox_to_analyze_right(Vox,Vdim,Vsize); 0109 end; 0110 0111 % --- Talairach 0112 % 0113 case 'talairach' 0114 if exist('Vtal', 'var') 0115 Vout = Vtal; 0116 else 0117 xyzfile = [brain_id '.xyz.mat']; 0118 if exist(xyzfile, 'file') 0119 load(xyzfile, 'XYZtal'); 0120 Vout = XYZtal; 0121 else 0122 Vout = []; 0123 end; 0124 end; 0125 0126 % --- MNI 0127 % 0128 case 'mni' 0129 if exist('Vmni', 'var') 0130 Vout = Vmni; 0131 else 0132 xyzfile = [brain_id '.xyz.mat']; 0133 if exist(xyzfile, 'file') 0134 load(xyzfile, 'XYZmm'); 0135 Vout = XYZmm; 0136 else 0137 Vout = []; 0138 end; 0139 end; 0140 0141 if isfield(F,'Fmni') 0142 F = F.Fmni; 0143 end 0144 case 'subj' 0145 warning('off', 'MATLAB:load:variableNotFound'); 0146 load(brainfile, 'subj'); 0147 warning('on', 'MATLAB:load:variableNotFound'); 0148 if exist('subj', 'var') 0149 % for V2.x format 0150 Vout = subj.V; 0151 F = subj.F; 0152 xx = subj.xx; 0153 inf_C = []; 0154 if isfield(subj, 'xxA') 0155 % v2.1 format 0156 xxA = subj.xxA; 0157 else 0158 % v2.0 format 0159 % xxA is standard brain's one. 0160 end 0161 else 0162 % for V1 format 0163 [Vout,F,xx,inf_C,xxA]= vb_load_cortex(brainfile); 0164 end 0165 otherwise 0166 if ~exist('Vall'), 0167 error('Unknown coord_type : %s', coord_type); 0168 end; 0169 0170 Vout = []; 0171 for i=1:length(Vall.key) 0172 if strcmp(Vall.key{i},coord_type), 0173 Vout = Vall.V{i}; 0174 break; 0175 end; 0176 end; 0177 0178 if isempty(Vout), 0179 error('Unknown coord_type : %s', coord_type); 0180 end; 0181 end; 0182 0183 return; 0184 0185 % 0186 % --- END OF MAIN PROCEDURE -------------------------------------------------- % 0187 0188 % --- INNER FUNCTIONS -------------------------------------------------------- % 0189 % 0190 % --- inner_check_brainfile() 0191 % 0192 function [brain_id] = inner_check_brainfile(brainfile) 0193 0194 if isempty(brainfile), error('brainfile is a required parameter'); end; 0195 0196 if ~isempty( findstr(brainfile, '.brain.mat') ) 0197 brain_id = brainfile(1:findstr(brainfile, '.brain.mat')-1); 0198 else 0199 error(['Brain file name is not correct:' brainfile]); 0200 end 0201 0202 if exist(brainfile, 'file') ~= 2 0203 error('cannot read brainfile : %s', brainfile); 0204 end 0205 % 0206 % --- end of inner_check_brainfile() 0207 0208 %%% END OF FILE %%%