Template script of how to run "atlas2vb"
"atlas2vb" is a program to get MNI and Talairach coordinate, and anatomical region
label for each cortical vertex point of individual brain coordinate
transformation to MNI-normalized-space.
1. Back-transform cortex coordinate 'V' in brainfile
to MNI-space coordinate and Talairach coordinate
2. Create an areafile based on the anatomical divisions
2006/03/01 by M.Sato
2006/03/01 by O. Yamashita
2007/03/05 by O. Yamashita
* MNI coordinate is stored in brainfile.
* save_xyzfile is removed.
* addpath(spm_dir) is removed
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 % Template script of how to run "atlas2vb" 0002 % 0003 % "atlas2vb" is a program to get MNI and Talairach coordinate, and anatomical region 0004 % label for each cortical vertex point of individual brain coordinate 0005 % transformation to MNI-normalized-space. 0006 % 0007 % 1. Back-transform cortex coordinate 'V' in brainfile 0008 % to MNI-space coordinate and Talairach coordinate 0009 % 2. Create an areafile based on the anatomical divisions 0010 % 0011 % 2006/03/01 by M.Sato 0012 % 2006/03/01 by O. Yamashita 0013 % 2007/03/05 by O. Yamashita 0014 % * MNI coordinate is stored in brainfile. 0015 % * save_xyzfile is removed. 0016 % * addpath(spm_dir) is removed 0017 % 0018 % Copyright (C) 2011, ATR All Rights Reserved. 0019 % License : New BSD License(see VBMEG_LICENSE.txt) 0020 0021 clear all 0022 close all 0023 pack 0024 0025 % MRIcro include 1x1x1 mm T1 MRI scan. 0026 % brodmann.img : 1x1x1 mm version of 'TD_brodmann' 0027 % aal.img : 1x1x1 mm version of 'aal_MNI_V4' 0028 % betmask.img : scalp mask image (2x2x2 mm) using for coordinate transform 0029 0030 0031 %--- Add SPM path if you do not installed SPM 0032 %--- Necessary function : spm_dctmtx (Creates basis functions for Discrete Cosine Transform.) 0033 %spm_dir = '/home/dcfs2/oyamashi/matlab/spm2/'; 0034 %addpath(spm_dir); 0035 0036 %---Set parameters required (filenames, atlas_id and so on) 0037 0038 % Atlas template file and ID 0039 0040 ATLAS_ID = {'aal', 'brodmann'}; 0041 atlas_id = ATLAS_ID{2}; % ATLAS_ID{1} or ATLAS_ID{2} 0042 0043 atlas_dir = 'MNI_atlas_templates/'; 0044 atlas_text = [atlas_id '.txt']; 0045 atlas_file = [atlas_id '.img']; 0046 mask_file = ['betmask.img']; % constant 0047 0048 % Subject brain file 0049 brain_dir = './'; 0050 brainfile = ['test.brain.mat']; 0051 sn_dir = './'; 0052 snfile = ['3d_sn.mat']; 0053 0054 %------------------------------------------------------- 0055 % You don't need to modify lines below 0056 %------------------------------------------------------- 0057 0058 % The names of save files are determined by 'brain_id' and 'atlas_id' automatically 0059 % If you want to change output filenames, please set 'save_areafile', 0060 % 'save_atlasfile' and 'save_xyzfile' below as you like. 0061 0062 EXT_brain = '.brain.mat'; 0063 EXT_xyz = '.xyz.mat'; 0064 EXT_atlas = '.atlas.mat'; 0065 brain_id = brainfile(1:findstr(brainfile,EXT_brain)-1); 0066 save_areafile = [brain_dir, brain_id '_' atlas_id '.area.mat']; 0067 save_atlasfile = [brain_dir, brain_id '_atlas.act.mat']; % Atlas label 0068 %save_xyzfile = [brain_dir, brain_id EXT_xyz]; % MNI coordinate 0069 0070 %--- Set parm struct 0071 parm.atlas_dir = atlas_dir; 0072 parm.atlas_id = atlas_id; 0073 parm.atlas_text = [atlas_dir, atlas_text]; 0074 parm.atlas_file = [atlas_dir, atlas_file]; 0075 parm.mask_file = [atlas_dir, mask_file]; 0076 parm.brainfile = [brain_dir, brainfile]; 0077 parm.snfile = [sn_dir, snfile]; 0078 parm.save_areafile = save_areafile; 0079 parm.save_atlasfile = save_atlasfile; 0080 %parm.save_xyzfile = save_xyzfile; 0081 parm.Rlimit = 4; % Max radius to check minimum distance to corresponding point [mm] 0082 parm.Rmax = 2; % Max radius to search corresponding point [mm] in the 1st-step 0083 0084 %parm = set_atlas_parm(atlas_dir,atlas_id,brain_dir,brainfile,snfile); 0085 0086 0087 %--- Back-transform cortex coordinate 'V' in brainfile 0088 %--- to MNI-space coordinate and Talairach coordinate 0089 0090 tic 0091 0092 D=load(parm.brainfile); 0093 0094 if ~isfield(D,'Vmni') 0095 [Vmni, Vtal, derr, IMGinfo] = vb_calc_mni_coord(parm); 0096 vb_save([parm.brain_file],'Vmni','Vtal','derr'); 0097 end 0098 0099 vb_ptime(toc) 0100 pack 0101 0102 %--- Create an areafile based on the anatomical template 0103 0104 tic 0105 0106 if strcmp(atlas_id, 'aal') == 1, 0107 vb_atlas2vb_aal(parm); 0108 else 0109 vb_atlas2vb(parm); 0110 end 0111 0112 vb_ptime(toc) 0113 0114 vb_plot_atlas(parm.brainfile, parm.save_atlasfile,atlas_id); 0115 0116 return