dmri_process_T1_freesurfer

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

0001 function dmri_process_T1_freesurfer(p)
0002 %
0003 % Copyright (C) 2011, ATR All Rights Reserved.
0004 % License : New BSD License(see VBMEG_LICENSE.txt)
0005 
0006 
0007 disp(mfilename);
0008 
0009 %
0010 % --- Previous check
0011 %
0012 if isfield(p, 'ref_fs_dir')
0013     if exist(p.ref_fs_dir, 'dir') == 7
0014         warning('FreeSurfer directory specified. skip creating.');
0015         return;
0016     elseif ~isempty(p.ref_fs_dir)
0017         error('Specified Freesurfer directory not found.');
0018     end
0019 end
0020 
0021 freesurfer_dir = fullfile(p.output_dir, p.fs_dirname, p.fs_sbj_name);
0022 if exist(freesurfer_dir, 'dir') == 7
0023     warning('FreeSurfer directory already exist. skip creating.');
0024     return;
0025 end
0026 
0027 %
0028 % --- Create cortex data using FreeSurfer
0029 %
0030 if isfield(p, 'ref_mri_file') && ~isempty(p.ref_mri_file)
0031     mri_file = p.ref_mri_file;
0032 else
0033     mri_file = fullfile(p.output_dir, p.t1_dirname, ['m', p.t1_file]);
0034 end
0035 if exist(mri_file, 'file') ~= 2
0036     error('Specified MRI file not found:%s', mri_file);
0037 end
0038 
0039 fs_root_dir      = fullfile(p.output_dir, p.fs_dirname);
0040 subj_id          = p.fs_sbj_name;
0041 
0042 % FreeSurfer
0043 if exist(fs_root_dir, 'dir') ~= 7
0044     vb_mkdir(fs_root_dir);
0045 end
0046 vb_freesurfer_run(mri_file, fs_root_dir, subj_id);