calculate_fodf

 Calculate fiber orientation density function (fodf)

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

0001 function calculate_fodf(p)
0002 % Calculate fiber orientation density function (fodf)
0003 %
0004 % Copyright (C) 2011, ATR All Rights Reserved.
0005 % License : New BSD License(see VBMEG_LICENSE.txt)
0006 
0007 disp(mfilename);
0008 
0009 % Get area for response function estimation
0010 dmri_root = fullfile(p.proj_root, p.dmri_dirname);
0011 fa_file = fullfile(dmri_root, p.dmri_dirname, [p.FA_basename, '.nii.gz']);
0012 resp_area_file = fullfile(dmri_root, p.fiber_track_dirname, p.fiber_resp_area_file);
0013 
0014 dmri_response_estimation_prepare(fa_file, resp_area_file);
0015 
0016 % Calculate fiber orientation density function.
0017 dmri_file = fullfile(dmri_root, p.dmri_dirname, [p.dmri_basename, '_m.nii.gz']);
0018 bval_file = fullfile(dmri_root, p.dmri_dirname, [p.dmri_basename, '_m.bval']);
0019 bvec_file = fullfile(dmri_root, p.dmri_dirname, [p.dmri_basename, '_m.bvec']);
0020 struct_brain_on_fa_file = fullfile(dmri_root, p.dmri_dirname, [p.struct_name, '_brain_FA.nii.gz']);
0021 output_mif_file = fullfile(dmri_root, p.fiber_track_dirname, p.fiber_mif_file);
0022 
0023 dmri_fodf_calc(dmri_file, bval_file, bvec_file, ...
0024                resp_area_file, struct_brain_on_fa_file, output_mif_file);
0025 
0026 % Check 1
0027 cmd = ['fslview ', struct_brain_on_fa_file, ' ', resp_area_file, ' -l Blue'];
0028 dmri_system(cmd);
0029 
0030 % Check 2
0031 % dmri_mrview(fa_file);