vb_freesurfer_run

 Run FreeSurfer to get all files for VBMEG.
 [Usage]
    vb_freesurfer_run(mri_file, fs_root_dir, subj_id)
 [Input]
          mri_file : Input MRI T1 Image file name.
                     This file should be created using convert_dicom_nifti.m
                      - NIfTI file(.nii)
                      - LAS Analyze file(.hdr/.img)
       fs_root_dir : Root Dir for FS data.
           subj_id : Subject ID , it becomes Sub-directory name.

 [Output files]
  fs_root_dir/subj_id/bem/
    - brain(cortex) model file
     lh.smoothwm.asc : smooth cortical surface
     rh.smoothwm.asc
     lh.inflated.asc : inflated surface
     rh.inflated.asc
     lh.curv.asc     : curvature info file
     rh.curv.asc
     lh.white.asc    : cortical surface
     rh.white.asc

    - skull surface for BEM
     inner_skull_surface.asc : inner skull surface
     outer_skull_surface.asc : outer skull surface
     outer_skin_surface.asc  : skin surface

    - spherical registration surface
     lh.sphere.reg.asc 
     rh.sphere.reg.asc


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

0001 function vb_freesurfer_run(mri_file, fs_root_dir, subj_id)
0002 % Run FreeSurfer to get all files for VBMEG.
0003 % [Usage]
0004 %    vb_freesurfer_run(mri_file, fs_root_dir, subj_id)
0005 % [Input]
0006 %          mri_file : Input MRI T1 Image file name.
0007 %                     This file should be created using convert_dicom_nifti.m
0008 %                      - NIfTI file(.nii)
0009 %                      - LAS Analyze file(.hdr/.img)
0010 %       fs_root_dir : Root Dir for FS data.
0011 %           subj_id : Subject ID , it becomes Sub-directory name.
0012 %
0013 % [Output files]
0014 %  fs_root_dir/subj_id/bem/
0015 %    - brain(cortex) model file
0016 %     lh.smoothwm.asc : smooth cortical surface
0017 %     rh.smoothwm.asc
0018 %     lh.inflated.asc : inflated surface
0019 %     rh.inflated.asc
0020 %     lh.curv.asc     : curvature info file
0021 %     rh.curv.asc
0022 %     lh.white.asc    : cortical surface
0023 %     rh.white.asc
0024 %
0025 %    - skull surface for BEM
0026 %     inner_skull_surface.asc : inner skull surface
0027 %     outer_skull_surface.asc : outer skull surface
0028 %     outer_skin_surface.asc  : skin surface
0029 %
0030 %    - spherical registration surface
0031 %     lh.sphere.reg.asc
0032 %     rh.sphere.reg.asc
0033 %
0034 %
0035 % Copyright (C) 2011, ATR All Rights Reserved.
0036 % License : New BSD License(see VBMEG_LICENSE.txt)
0037 
0038 if nargin < 3
0039     eval(['help ' mfilename]);
0040     return;
0041 end
0042 
0043 %
0044 % --- Previous check
0045 %
0046 
0047 if exist(fs_root_dir, 'dir') ~= 7
0048     error('fs_root_dir not found : %s', fs_root_dir);
0049 end
0050 if strfind(subj_id, ' ')
0051     error('subj_id contains white space : %s', subj_id);
0052 end
0053 if exist(mri_file, 'file') ~= 2
0054     error('mri_file not found : %s', mri_file);
0055 end
0056 
0057 if strcmp(mri_file(end-3:end), '.hdr')
0058     mri_file(end-3:end) = '.img';
0059 end
0060 
0061 %
0062 % --- Main Procedure
0063 %
0064 
0065 % give a script permission for execution.
0066 cmd = which('RunFreeSurfer.csh');
0067 [result, err_txt] = system(['chmod 755 ' cmd]);
0068 if result ~= 0
0069     error(err_txt);
0070 end
0071 dest_dir = fullfile(fs_root_dir, subj_id);
0072 if exist(dest_dir, 'dir') == 7
0073     warning('FreeSurfer directory already exist. skip creating. :%s', dest_dir);
0074     return;
0075 end
0076 exe_cmd = [cmd, ' ', ...
0077            fs_root_dir, ' ',...
0078            subj_id, ' ', ...
0079            mri_file, ' ', ...
0080            '$FREESURFER_HOME'];
0081 
0082 dmri_system(exe_cmd, '-echo');