create_mask_for_fiber_tracking

 Create mask for fiber tracking

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

0001 function create_mask_for_fiber_tracking(p)
0002 % Create mask for fiber tracking
0003 %
0004 % Copyright (C) 2011, ATR All Rights Reserved.
0005 % License : New BSD License(see VBMEG_LICENSE.txt)
0006 
0007 disp(mfilename);
0008 
0009 % Create White matter volume file on FA coordinate system
0010 fs_dir = fullfile(p.proj_root, p.fs_dirname, p.struct_name);
0011 dmri_root = fullfile(p.proj_root, p.dmri_dirname);
0012 ref_brain_file = fullfile(dmri_root, p.t1_dirname,  [p.struct_name '_brain.nii.gz']);
0013 ref_FA_file = fullfile(dmri_root, p.dmri_dirname, [p.FA_basename '.nii.gz']);
0014 trans_info_dir = fullfile(dmri_root, p.transform_info_dirname);
0015 
0016 wm_file = fullfile(dmri_root, p.fiber_track_dirname, 'wm.nii.gz');
0017 
0018 dmri_wm_FA_volume_create(fs_dir, ...
0019                         ref_brain_file, ref_FA_file, trans_info_dir, ...
0020                         wm_file);
0021 
0022 %  Merge Parcel all + White matter
0023 parcel_all_file = fullfile(dmri_root, p.parcels_dirname, 'parcel_all.nii.gz');
0024 parcel_wm_file  = fullfile(dmri_root, p.fiber_track_dirname, p.fiber_mask_file);
0025 
0026 % parcel_all_file + wm_file = parcel_wm_file
0027 dmri_merge_parcels_wm(parcel_all_file, wm_file, parcel_wm_file);