Incorporate SPM voxel file (.spm.mat). (VBMEG public function) This function incoporates SPM voxel file, which include position and t-value for voxels at which its activity is statistically significant. Coordinate system of voxel is assumed to be VBMEG coordinate system (direction: RAS, origin: center of structural MRI volume). Voxel values are mapped onto the cortical surface model. [syntax] vb_job_fmri(proj_root, fmri_parm) [input] proj_root: <<string>> VBMEG project root directory. fmri_parm: <<struct>> Parameters for fmri incorporation. --- fields of fmri_parm brain_file : <<string>> Cortical surface model file (.brain.mat). act_file : <<string>> Cortical activity map file (.act.mat). area_file : <<string>> Cortical area file (.area.mat). spm_file : <<string>> SPM voxel file (.spm.mat). fmri_id : <<string>> Identifier of activity map. area_id : <<string>> Identifier of cortical area. comment : <<string>> Any comment. SPM_Radius : <<float>> A parameter of mapping algorithm. SPM_zstep : <<float>> A parameter of mapping algorithm. Gauss_radius: <<float>> A parameter of mapping algorithm. Gauss_max : <<float>> A parameter of mapping algorithm. --- [output] Activity map on the cortical surface is registered to cortical activity map file (.area.mat). In addition, Area on the cortical surface of SPM voxel data is registered to cortical area file (.area.mat). [note] Important for VBMEG0.8 or older users: In old versions of VBMEG, coordinate system of SPM voxel file was LAS. Although SPM voxel file created by vb_job_convert_spm.m with old versions is supported, it is strongly recommended that you re-create SPM voxel file by the latest version of VBMEG. [history] 2010-06-03 Taku Yoshioka Minor change (verbose level support) Copyright (C) 2011, ATR All Rights Reserved. License : New BSD License(see VBMEG_LICENSE.txt)
0001 function vb_job_fmri(proj_root, fmri_parm) 0002 % Incorporate SPM voxel file (.spm.mat). 0003 % (VBMEG public function) 0004 % 0005 % This function incoporates SPM voxel file, which include position 0006 % and t-value for voxels at which its activity is statistically 0007 % significant. Coordinate system of voxel is assumed to be VBMEG 0008 % coordinate system (direction: RAS, origin: center of structural MRI 0009 % volume). Voxel values are mapped onto the cortical surface model. 0010 % 0011 % [syntax] 0012 % vb_job_fmri(proj_root, fmri_parm) 0013 % 0014 % [input] 0015 % proj_root: <<string>> VBMEG project root directory. 0016 % fmri_parm: <<struct>> Parameters for fmri incorporation. 0017 % --- fields of fmri_parm 0018 % brain_file : <<string>> Cortical surface model file (.brain.mat). 0019 % act_file : <<string>> Cortical activity map file (.act.mat). 0020 % area_file : <<string>> Cortical area file (.area.mat). 0021 % spm_file : <<string>> SPM voxel file (.spm.mat). 0022 % fmri_id : <<string>> Identifier of activity map. 0023 % area_id : <<string>> Identifier of cortical area. 0024 % comment : <<string>> Any comment. 0025 % SPM_Radius : <<float>> A parameter of mapping algorithm. 0026 % SPM_zstep : <<float>> A parameter of mapping algorithm. 0027 % Gauss_radius: <<float>> A parameter of mapping algorithm. 0028 % Gauss_max : <<float>> A parameter of mapping algorithm. 0029 % --- 0030 % 0031 % [output] 0032 % Activity map on the cortical surface is registered to cortical activity 0033 % map file (.area.mat). In addition, Area on the cortical surface of SPM 0034 % voxel data is registered to cortical area file (.area.mat). 0035 % 0036 % [note] 0037 % Important for VBMEG0.8 or older users: In old versions of VBMEG, 0038 % coordinate system of SPM voxel file was LAS. Although SPM voxel file 0039 % created by vb_job_convert_spm.m with old versions is supported, it is 0040 % strongly recommended that you re-create SPM voxel file by the latest 0041 % version of VBMEG. 0042 % 0043 % [history] 0044 % 2010-06-03 Taku Yoshioka 0045 % Minor change (verbose level support) 0046 % 0047 % Copyright (C) 2011, ATR All Rights Reserved. 0048 % License : New BSD License(see VBMEG_LICENSE.txt) 0049 0050 proj_root = vb_rm_trailing_slash(proj_root); 0051 0052 % 0053 % Verbose level 0054 % 0055 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0056 global vbmeg_inst; 0057 const = vb_define_verbose; 0058 if isfield(vbmeg_inst,'verbose_level'), 0059 verbose_level = vbmeg_inst.verbose_level; 0060 else 0061 verbose_level = const.VERBOSE_LEVEL_NOTICE; 0062 end 0063 0064 % 0065 % Do not modify following lines 0066 % 0067 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0068 % 0069 % make fMRI data 0070 % brain_parm.act_file : fMRI activity file 0071 0072 act_file = [proj_root '/' fmri_parm.act_file ]; 0073 area_file = [proj_root '/' fmri_parm.area_file ]; 0074 0075 [fMRINew, AreaNew, SPM] = vb_make_fmri_data(proj_root, fmri_parm); 0076 0077 vb_add_act([act_file],fMRINew); 0078 vb_add_area([area_file],AreaNew); 0079 0080 % Check fMRI activity 0081 if verbose_level>=const.VERBOSE_LEVEL_NOTICE, 0082 vb_check_fmri(proj_root,fmri_parm); 0083 end 0084 0085 % Check voxel mapping 0086 %load([proj_root filesep fmri_parm.brain_file],'V'); 0087 %XYZmm = SPM.XYZmm*1e-3; 0088 %figure; 0089 %title_str = {'Top view','Back view','Left view','Right view'}; 0090 %v = [0 90; 0 0; -90 0; 90 0]; 0091 %for i=1:4 0092 % subplot(2,2,i); 0093 % plot3(V(:,1),V(:,2),V(:,3),'r.'); hold on; 0094 % plot3(XYZmm(1,:),XYZmm(2,:),XYZmm(3,:),'b.'); 0095 % view(v(i,:)); 0096 % title(title_str{i}); 0097 % axis equal; 0098 %end 0099 0100 % project_file save 0101 proj_file = get_project_filename; 0102 if isempty(proj_file) 0103 return; 0104 end 0105 0106 project_file_mgr('load', proj_file); 0107 project_file_mgr('add', 'fmri_parm', fmri_parm);