extract_brain_from_T1

 Extract brain from T1 image

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

0001 function extract_brain_from_T1(p)
0002 % Extract brain from T1 image
0003 %
0004 % Copyright (C) 2011, ATR All Rights Reserved.
0005 % License : New BSD License(see VBMEG_LICENSE.txt)
0006 
0007 disp(mfilename);
0008 
0009 % Set parameters
0010 t1_parm.mri_file = fullfile(p.proj_root, p.t1_dirname, ['m' p.struct_name '.nii']);
0011 t1_parm.threshold = 0.5;% threshold value to extract brain mask (from 0 to 1.0)
0012 t1_parm.output_dir = fullfile(p.proj_root, p.dmri_dirname, p.t1_dirname);
0013 t1_parm.output_basename = p.struct_name;
0014 
0015 % Extract brain from T1 image
0016 dmri_job_t1_preprocess(t1_parm);
0017 
0018 % Check skull stripped brain image.
0019 cmd = ['fslview ' ...
0020        fullfile(t1_parm.output_dir, [t1_parm.output_basename, '_brain.nii.gz']) ' ', ...
0021        fullfile(t1_parm.output_dir, [t1_parm.output_basename, '.nii.gz'])];
0022 dmri_system(cmd);