dmri_process_T1_brain_extract

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

0001 function dmri_process_T1_brain_extract(p)
0002 %
0003 % Copyright (C) 2011, ATR All Rights Reserved.
0004 % License : New BSD License(see VBMEG_LICENSE.txt)
0005 disp(mfilename);
0006 
0007 %
0008 % --- Convert T1 to FSL format(nii.gz) and Skull stripped brain
0009 %
0010 if isfield(p, 'ref_mri_file') && ~isempty(p.ref_mri_file)
0011     mri_file = p.ref_mri_file;
0012 else
0013     mri_file = fullfile(p.output_dir, p.t1_dirname, ['m', p.t1_file]);
0014 end
0015 
0016 t1_parm.mri_file         = mri_file;
0017 t1_parm.threshold        = p.t1_brain_threshold;
0018 t1_parm.output_dir       = fullfile(p.output_dir, p.t1_dirname);
0019 t1_parm.output_basename  = p.t1_brain_basename;
0020 
0021 dmri_job_t1_preprocess(t1_parm);
0022 
0023 % Check skull stripped brain image.
0024 cmd = ['fslview ' ...
0025        fullfile(t1_parm.output_dir, [p.t1_brain_basename, '_brain.nii.gz']) ' ', ...
0026        fullfile(t1_parm.output_dir, [p.t1_brain_basename, '.nii.gz'])];
0027 dmri_system(cmd);