dmri_process_fiber_tracking_mask_create

 Create Fiber tracking mask file

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

0001 function dmri_process_fiber_tracking_mask_create(p)
0002 % Create Fiber tracking mask file
0003 %
0004 % Copyright (C) 2011, ATR All Rights Reserved.
0005 % License : New BSD License(see VBMEG_LICENSE.txt)
0006 
0007 disp(mfilename);
0008 
0009 %
0010 % --- Create White matter volume file on FA coordinate system.
0011 %
0012 if isfield(p, 'ref_fs_dir') && ~isempty(p.ref_fs_dir)
0013     fs_dir = p.ref_fs_dir;
0014 else
0015     fs_dir = fullfile(p.output_dir, p.fs_dirname, p.fs_sbj_name);
0016 end
0017 
0018 ref_brain_file  = fullfile(p.output_dir, p.t1_dirname, [p.t1_brain_basename '_brain.nii.gz']);
0019 ref_FA_file     = fullfile(p.output_dir, p.dwi_dirname, [p.FA_basename, '.nii.gz']);
0020 trans_info_dir  = fullfile(p.output_dir, p.transform_info_dirname);
0021 
0022 wm_file         = fullfile(p.output_dir, p.fiber_track_dirname, 'wm.nii.gz');
0023 
0024 dmri_wm_FA_volume_create(fs_dir, ...
0025                         ref_brain_file, ref_FA_file, trans_info_dir, ...
0026                         wm_file);
0027 
0028 %
0029 % --- Merge Parcel all + White matter
0030 %
0031 parcel_all_file = fullfile(p.output_dir, p.parcels_dirname, 'parcel_all.nii.gz');
0032 parcel_wm_file  = fullfile(p.output_dir, p.fiber_track_dirname, p.fiber_mask_file);
0033 
0034 % parcel_all_file + wm_file = parcel_wm_file
0035 dmri_merge_parcels_wm(parcel_all_file, wm_file, parcel_wm_file);