dmri_process_FA_image_clean

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

0001 function dmri_process_FA_image_clean(p)
0002 %
0003 % Copyright (C) 2011, ATR All Rights Reserved.
0004 % License : New BSD License(see VBMEG_LICENSE.txt)
0005 
0006 disp(mfilename);
0007 
0008 %
0009 % --- Transform T1-struct brain and brain mask image into FA coordinate system.
0010 %
0011 from_file        = fullfile(p.output_dir, p.t1_dirname, [p.t1_brain_basename, '_brain_mask.nii.gz']);
0012 brain_mask_file  = fullfile(p.output_dir, p.dwi_dirname, [p.t1_brain_basename, '_brain_mask_FA.nii.gz']);
0013 to_ref_file      = fullfile(p.output_dir, p.dwi_dirname, [p.FA_coreg_basename, '.nii.gz']);
0014 direction        = 'struct2fa_nointerp';
0015 transinfo_dir    = fullfile(p.output_dir, p.transform_info_dirname);
0016 dmri_image_transform(from_file, brain_mask_file, to_ref_file, ...
0017                             direction, transinfo_dir);
0018 
0019 from_file     = fullfile(p.output_dir, p.t1_dirname,  [p.t1_brain_basename, '_brain.nii.gz']);
0020 brain_file    = fullfile(p.output_dir, p.dwi_dirname, [p.t1_brain_basename, '_brain_FA.nii.gz']);
0021 to_ref_file   = fullfile(p.output_dir, p.dwi_dirname, [p.FA_coreg_basename, '.nii.gz']);
0022 direction     = 'struct2fa';
0023 transinfo_dir = fullfile(p.output_dir, p.transform_info_dirname);
0024 dmri_image_transform(from_file, brain_file, to_ref_file, ...
0025                             direction, transinfo_dir);
0026 
0027 
0028 %
0029 % --- Create clean FA image
0030 %
0031 dwi_file        = fullfile(p.output_dir, p.dwi_dirname, [p.dwi_basename, '_m.nii.gz']);
0032 bval_file       = fullfile(p.output_dir, p.dwi_dirname, [p.dwi_basename, '_m.bval']);
0033 bvec_file       = fullfile(p.output_dir, p.dwi_dirname, [p.dwi_basename, '_m.bvec']);
0034 output_dir      = fullfile(p.output_dir, p.dwi_dirname);
0035 output_name     = p.FA_basename;
0036 
0037 dmri_FA_image_create(dwi_file, ...
0038                      bval_file, bvec_file, ...
0039                      brain_mask_file, ...
0040                      output_dir, ...
0041                      output_name);
0042 
0043 % output_root/DWI/data_FA.nii.gz
0044 
0045 
0046 % Check1. cleaned FA image by fslview
0047 fa_file        = fullfile(p.output_dir, p.dwi_dirname, [p.FA_basename, '.nii.gz']);
0048 fa_coreg_file  = fullfile(p.output_dir, p.dwi_dirname, [p.FA_coreg_basename, '.nii.gz']);
0049 cmd = ['fslview ', fa_file, ' ', fa_coreg_file];
0050 dmri_system(cmd);
0051 
0052 % Check2. coregistration
0053 cmd = ['fslview ', brain_file, ' ', fa_file];
0054 dmri_system(cmd);
0055 
0056 % Trouble shooting(.nii.gz should be converted into .nii using gunzip beforehand)
0057 % dmri_system('erode data_dwi_m_brain_mask.nii - | erode - - | erode - - | mrmult data_FA_coreg.nii - data_FA.nii');