Import FreeSurfer's sphere coordinate into cortical surface file.
(VBMEG public function)
FreeSurfer's cortical surface model has a (coregistered) sphere
coordinate values at each vertex. This function is used to import the
sphere coordinate values into an existing cortical surface file
(.brain.mat). Struct variables 'Vall' will be added to the cortical
surface model file (see [output]).
[syntax]
vb_job_brain_add_sphcoord(brain_parm)
vb_job_brain_add_sphcoord(proj_root,brain_parm)
[input]
proj_root : <<string>> VBMEG project root directory.
brain_parm: <<struct>> Parameters for import.
--- fields of brain_parm
brain_file: <<string>> Cortical surface model file
(.brain.mat). Struct variable 'Vall' will be added to this
file (see [output]).
brain_sphL: <<string>> Sphere surface file (.sphere.reg(.asc))
corresponding to the left hemisphere of the source
model.
brain_sphR: <<string>> Sphere surface file (.sphere.reg(.asc))
corresponding to the right hemisphere of the source
model.
key : <<string>> Arbitrary ID of the coordinate value
(e.g., 'Sphere_coreg'). It is used to load coordinate
values by vb_load_cortex.
---
[output]
Struct variable 'Vall' will be added to brain_parm.brain_file.
--- fields of Vall
V : <<cell of matrix>> Spherical coordinate values.
key: <<cell of string>> Used to get spherical coordinate values by
vb_load_cortex.
---
[example]
You can add sphere coordinate values to existing cortical surface model
file by the following code:
>> brain_parm.brain_file = 'existing_brain_file'; % .brain.mat
>> brain_parm.brain_sphL = 'lh.sphere.reg.asc';
>> brain_parm.brain_sphR = 'rh.sphere.reg.asc';
>> brain_parm.key = 'Sphere_coreg'; % arbitrary string available
>> proj_root = 'your_project_root_directory';
>> vb_job_brain_add_sphcoord(proj_root,brain_parm);
You can get the spherical coordinate values of the cortical surface
model by the following code:
>> V = vb_load_cortex('your_brain_file','Sphere_coreg');
[see also]
@see vb_load_cortex.m
[history]
2010-11-18 Taku Yoshioka
2010-12-22 taku-y
[minor] Bug fix: 'proj_root' attached with directroies specified by
'brain_parm.brain_file'.
2015-11-26 Masa-aki Sato
[change] original spherical coordinate is saved to Vall
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function vb_job_brain_add_sphcoord(varargin) 0002 % Import FreeSurfer's sphere coordinate into cortical surface file. 0003 % (VBMEG public function) 0004 % 0005 % FreeSurfer's cortical surface model has a (coregistered) sphere 0006 % coordinate values at each vertex. This function is used to import the 0007 % sphere coordinate values into an existing cortical surface file 0008 % (.brain.mat). Struct variables 'Vall' will be added to the cortical 0009 % surface model file (see [output]). 0010 % 0011 % [syntax] 0012 % vb_job_brain_add_sphcoord(brain_parm) 0013 % vb_job_brain_add_sphcoord(proj_root,brain_parm) 0014 % 0015 % [input] 0016 % proj_root : <<string>> VBMEG project root directory. 0017 % brain_parm: <<struct>> Parameters for import. 0018 % --- fields of brain_parm 0019 % brain_file: <<string>> Cortical surface model file 0020 % (.brain.mat). Struct variable 'Vall' will be added to this 0021 % file (see [output]). 0022 % brain_sphL: <<string>> Sphere surface file (.sphere.reg(.asc)) 0023 % corresponding to the left hemisphere of the source 0024 % model. 0025 % brain_sphR: <<string>> Sphere surface file (.sphere.reg(.asc)) 0026 % corresponding to the right hemisphere of the source 0027 % model. 0028 % key : <<string>> Arbitrary ID of the coordinate value 0029 % (e.g., 'Sphere_coreg'). It is used to load coordinate 0030 % values by vb_load_cortex. 0031 % --- 0032 % 0033 % [output] 0034 % Struct variable 'Vall' will be added to brain_parm.brain_file. 0035 % --- fields of Vall 0036 % V : <<cell of matrix>> Spherical coordinate values. 0037 % key: <<cell of string>> Used to get spherical coordinate values by 0038 % vb_load_cortex. 0039 % --- 0040 % 0041 % [example] 0042 % You can add sphere coordinate values to existing cortical surface model 0043 % file by the following code: 0044 % 0045 % >> brain_parm.brain_file = 'existing_brain_file'; % .brain.mat 0046 % >> brain_parm.brain_sphL = 'lh.sphere.reg.asc'; 0047 % >> brain_parm.brain_sphR = 'rh.sphere.reg.asc'; 0048 % >> brain_parm.key = 'Sphere_coreg'; % arbitrary string available 0049 % >> proj_root = 'your_project_root_directory'; 0050 % >> vb_job_brain_add_sphcoord(proj_root,brain_parm); 0051 % 0052 % You can get the spherical coordinate values of the cortical surface 0053 % model by the following code: 0054 % 0055 % >> V = vb_load_cortex('your_brain_file','Sphere_coreg'); 0056 % 0057 % [see also] 0058 % @see vb_load_cortex.m 0059 % 0060 % [history] 0061 % 2010-11-18 Taku Yoshioka 0062 % 2010-12-22 taku-y 0063 % [minor] Bug fix: 'proj_root' attached with directroies specified by 0064 % 'brain_parm.brain_file'. 0065 % 2015-11-26 Masa-aki Sato 0066 % [change] original spherical coordinate is saved to Vall 0067 % 0068 % Copyright (C) 2011, ATR All Rights Reserved. 0069 % License : New BSD License(see VBMEG_LICENSE.txt) 0070 0071 % 0072 % check input arguments 0073 % 0074 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0075 if length(varargin) == 1 0076 proj_root = []; 0077 brain_parm = varargin{1}; 0078 elseif length(varargin) == 2 0079 proj_root = varargin{1}; 0080 brain_parm = varargin{2}; 0081 else 0082 error('Error: invalid usage of vb_job_brain_sphcoord.'); 0083 end; 0084 0085 if ~isempty(proj_root), 0086 proj_root = vb_rm_trailing_slash(proj_root); 0087 end; 0088 0089 % 0090 % Make absolute path 0091 % 0092 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0093 brain_parm_abs = brain_parm; 0094 0095 if isempty(proj_root) 0096 brain_parm_abs.brain_file = [brain_parm.brain_file]; 0097 else 0098 brain_parm_abs.brain_file = [proj_root filesep brain_parm.brain_file]; 0099 end 0100 % 0101 % Verbose level 0102 % 0103 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0104 global vbmeg_inst 0105 verbose_const = vb_define_verbose; 0106 0107 if isempty(vbmeg_inst) | ~isfield(vbmeg_inst,'verbose_level'), 0108 verbose_level = verbose_const.VERBOSE_LEVEL_NOTICE; 0109 else 0110 verbose_level = vbmeg_inst.verbose_level; 0111 end; 0112 0113 % 0114 % Load coordinate values 0115 % 0116 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0117 [tmp1,tmp2,ix_V_org] = vb_load_cortex_info(brain_parm_abs.brain_file); 0118 0119 VL0 = vb_fs_load_surface(brain_parm_abs.brain_sphL); 0120 VR0 = vb_fs_load_surface(brain_parm_abs.brain_sphR); 0121 0122 % [change] original spherical coordinate is saved to Vall 0123 V0 = [VL0; VR0]; 0124 0125 % spherical coordinate corresponding to cortical vertex 0126 VL = VL0(ix_V_org.Left,:); 0127 VR = VR0(ix_V_org.Right-size(VL0,1),:); 0128 0129 V = [VL; VR]; 0130 % 0131 % Add coordinate values 0132 % 0133 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0134 S = load(brain_parm_abs.brain_file); 0135 if isfield(S,'Vall'), 0136 Vall = S.Vall; 0137 else 0138 Vall.V = cell(0); 0139 Vall.key = cell(0); 0140 end; 0141 0142 flag = true; 0143 flag_org = true; 0144 0145 for i=1:length(Vall.key) 0146 if strcmp(Vall.key{i},brain_parm_abs.key), 0147 flag = false; 0148 Vall.V{i} = V; 0149 % if verbose_level>=verbose_const.VERBOSE_LEVEL_NOTICE, 0150 % msg = ['Brain coordinate ID ''' brain_parm_abs.key ... 0151 % ''' is already used. Overwrite ?']; 0152 % str = questdlg(msg,'Brain coordinate registration','Yes', ... 0153 % 'Cancel','Cancel'); 0154 % if strcmp(str,'Yes') 0155 % Vall.V{i} = V; 0156 % h = msgbox(['Brain coordinate ID ''' brain_parm_abs.key ... 0157 % ''' was overwritten.']); 0158 % uiwait(h); 0159 % end; 0160 % else 0161 vb_disp(['Brain coordinate ID ''' brain_parm_abs.key ... 0162 ''' is already ' ... 0163 'used, so it was overwritten with new data. '], ... 0164 verbose_const.VERBOSE_LEVEL_WARNING); 0165 % Vall.V{i} = V; 0166 % end; 0167 end; 0168 0169 if strcmp(Vall.key{i},'orig_sphere'), 0170 flag_org = false; 0171 end 0172 end; 0173 0174 if flag_org, 0175 Vall.V{length(Vall.key)+1} = V0; 0176 Vall.key{length(Vall.key)+1} = 'orig_sphere'; 0177 end; 0178 0179 if flag, 0180 Vall.V{length(Vall.key)+1} = V; 0181 Vall.key{length(Vall.key)+1} = brain_parm_abs.key; 0182 end; 0183 0184 vb_save(brain_parm_abs.brain_file,'Vall'); 0185 0186 % 0187 % project_file save 0188 % 0189 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0190 % proj_file = get_project_filename; 0191 % if isempty(proj_file) 0192 % return; 0193 % end; 0194 % 0195 % project_file_mgr('load', proj_file); 0196 % project_file_mgr('add', 'brain_parm', brain_parm); 0197 % 0198 % return;