dmri_process_cortex_import

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

0001 function dmri_process_cortex_import(p)
0002 %
0003 % Copyright (C) 2011, ATR All Rights Reserved.
0004 % License : New BSD License(see VBMEG_LICENSE.txt)
0005 
0006 disp(mfilename);
0007 
0008 %
0009 % --- Previous check
0010 %
0011 if isfield(p, 'ref_brain_file') && exist(p.ref_brain_file, 'file') == 2
0012     if isfield(p, 'ref_aal_area_file') && exist(p.ref_aal_area_file, 'file') == 2
0013         warning('VBMEG Cortical files creating step is skipped because p.ref_brain file specified.');
0014         return;
0015     end
0016 end
0017 if isfield(p, 'ref_brain_file') && ~isempty(p.ref_brain_file)
0018     error('Specified VBMEG cortical file not found. :%s', p.ref_brain_file);
0019 end
0020 if isfield(p, 'ref_aal_area_file') && ~isempty(p.ref_aal_area_file)
0021     error('Specified VBMEG AAL-area file not found. :%s', p.ref_aal_area_file);
0022 end
0023 
0024 % Start Importing freesurfer files
0025 start = tic;
0026 if isfield(p, 'ref_fs_dir') && ~isempty(p.ref_fs_dir)
0027     freesurfer_dir = p.ref_fs_dir;
0028 else
0029     freesurfer_dir = fullfile(p.output_dir, p.fs_dirname, p.fs_sbj_name);
0030 end
0031 if isfield(p, 'ref_mri_file') && ~isempty(p.ref_mri_file)
0032     mri_file = p.ref_mri_file;
0033 else
0034     mri_file = fullfile(p.output_dir, p.t1_dirname, ['m', p.t1_file]);
0035 end
0036 
0037 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0038 % not necessary to edit
0039 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0040 brain_parm = vb_set_brain_parm(); % get default parameter
0041 brain_parm.FS_left_file         = [freesurfer_dir, '/', 'bem/lh.smoothwm.asc'];
0042 brain_parm.FS_right_file        = [freesurfer_dir, '/', 'bem/rh.smoothwm.asc'];
0043 brain_parm.FS_left_infl_file    = [freesurfer_dir, '/', 'bem/lh.inflated.asc'];
0044 brain_parm.FS_right_infl_file   = [freesurfer_dir, '/', 'bem/rh.inflated.asc'];
0045 brain_parm.FS_left_curv_file    = [freesurfer_dir, '/', 'bem/lh.curv.asc'];
0046 brain_parm.FS_right_curv_file   = [freesurfer_dir, '/', 'bem/rh.curv.asc'];
0047 brain_parm.FS_left_sphere_file  = [freesurfer_dir, '/', 'bem/lh.sphere.reg.asc'];
0048 brain_parm.FS_right_sphere_file = [freesurfer_dir, '/', 'bem/rh.sphere.reg.asc'];
0049 brain_parm.FS_sphere_key        = 'sphere.reg';
0050 brain_parm.FS_left_label_file   = [freesurfer_dir, '/', 'label/lh.cortex.label'];
0051 brain_parm.FS_right_label_file  = [freesurfer_dir, '/', 'label/rh.cortex.label'];
0052 
0053 % registration method to standard brain model.
0054 %     = 'FS' : Freesurfer sphere file is used.
0055 brain_parm.registration_mode='FS';
0056 
0057 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0058 % Output directory/file settings
0059 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0060 proj_root = fullfile(p.output_dir, p.vbmeg_dirname);
0061 if exist(proj_root, 'dir') ~= 7
0062     mkdir(proj_root);
0063 end
0064 brain_parm.analyze_file = mri_file;
0065 brain_parm.brain_file = [p.vbmeg_cortex_basename, '.brain.mat'];
0066 brain_parm.area_file =  [p.vbmeg_cortex_basename, '.area.mat'];
0067 brain_parm.act_file =   [p.vbmeg_cortex_basename, '.act.mat'];
0068 
0069 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0070 % Cortical model import
0071 vb_job_brain(proj_root, brain_parm);
0072 
0073 toc(start);