remove_noise_in_fa

 Remove ambient noise in FA image by using brain mask extracted from T1

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

0001 function remove_noise_in_fa(p)
0002 % Remove ambient noise in FA image by using brain mask extracted from T1
0003 %
0004 % Copyright (C) 2011, ATR All Rights Reserved.
0005 % License : New BSD License(see VBMEG_LICENSE.txt)
0006 
0007 disp(mfilename);
0008 
0009 % Transform brain mask extracted from T1 image into FA coordinate system
0010 dmri_root = fullfile(p.proj_root, p.dmri_dirname);
0011 from_file = fullfile(dmri_root, p.t1_dirname, [p.struct_name '_brain_mask.nii.gz']);
0012 brain_mask_file = fullfile(dmri_root, p.dmri_dirname, [p.struct_name '_brain_mask_FA.nii.gz']);
0013 to_ref_file = fullfile(dmri_root, p.dmri_dirname, [p.FA_coreg_basename, '.nii.gz']);
0014 direction = 'struct2fa_nointerp';
0015 transinfo_dir = fullfile(dmri_root, p.transform_info_dirname);
0016 dmri_image_transform(from_file, brain_mask_file, to_ref_file, ...
0017                             direction, transinfo_dir);
0018 
0019 % Transform brain extracted from T1 image into FA coordinate system
0020 from_file = fullfile(dmri_root, p.t1_dirname,  [p.struct_name '_brain.nii.gz']);
0021 brain_file = fullfile(dmri_root, p.dmri_dirname, [p.struct_name '_brain_FA.nii.gz']);
0022 to_ref_file = fullfile(dmri_root, p.dmri_dirname, [p.FA_coreg_basename, '.nii.gz']);
0023 direction = 'struct2fa';
0024 transinfo_dir = fullfile(dmri_root, p.transform_info_dirname);
0025 dmri_image_transform(from_file, brain_file, to_ref_file, ...
0026                             direction, transinfo_dir);
0027 
0028 % Remove noise in FA image
0029 dmri_file = fullfile(dmri_root, p.dmri_dirname, [p.dmri_basename, '_m.nii.gz']);
0030 bval_file = fullfile(dmri_root, p.dmri_dirname, [p.dmri_basename, '_m.bval']);
0031 bvec_file = fullfile(dmri_root, p.dmri_dirname, [p.dmri_basename, '_m.bvec']);
0032 output_dir = fullfile(dmri_root, p.dmri_dirname);
0033 output_name = p.FA_basename;
0034 
0035 dmri_FA_image_create(dmri_file, ...
0036                      bval_file, bvec_file, ...
0037                      brain_mask_file, ...
0038                      output_dir, ...
0039                      output_name);
0040 
0041 % Check1. cleaned FA image by fslview
0042 fa_file        = fullfile(dmri_root, p.dmri_dirname, [p.FA_basename, '.nii.gz']);
0043 fa_coreg_file  = fullfile(dmri_root, p.dmri_dirname, [p.FA_coreg_basename, '.nii.gz']);
0044 cmd = ['fslview ', fa_file, ' ', fa_coreg_file];
0045 dmri_system(cmd);
0046 
0047 % Check2. coregistration
0048 cmd = ['fslview ', brain_file, ' ', fa_file];
0049 dmri_system(cmd);