extract_brain_from_dmri

 Make mask to extract brain from dMRI

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

0001 function extract_brain_from_dmri(p)
0002 % Make mask to extract brain from dMRI
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 parameter
0010 threshold =  0.18;% threshold value to extract brain mask from dMRI (from 0 to 1.0)
0011 
0012 % Set input file
0013 dmri_file = fullfile(p.proj_root, p.dmri_dirname, p.dmri_dirname, [p.dmri_basename, '_m.nii.gz']);
0014 
0015 % Extract brain from dMRI
0016 brain_image_extract(dmri_file, threshold);
0017 
0018 % Check by fslview
0019 brain_mask_file = fullfile(p.proj_root, p.dmri_dirname, p.dmri_dirname, [p.dmri_basename, '_m_brain_mask.nii.gz']);
0020 cmd = ['fslview ', dmri_file, ' ', brain_mask_file];
0021 dmri_system(cmd);