tutorial_fiber_tracking_for_movie_for_LCD

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

0001 %
0002 % Copyright (C) 2011, ATR All Rights Reserved.
0003 % License : New BSD License(see VBMEG_LICENSE.txt)
0004 
0005 root = 'data';
0006 
0007 % Load current and linear connectome dynamics model
0008 movie_current_file = fullfile(root, '/dynamics/input_for_movie/a.mat');
0009 load(movie_current_file, 'Z', 'B')
0010 
0011 
0012 % Choose strong pairs
0013 Npairs = 100;
0014 current_threshold = 0.1;
0015 [parcel_to_list,parcel_from_list] = dmri_select_pairs_for_movie(Z, B, Npairs, current_threshold);
0016 
0017 fprintf('Number of pairs : %d\n', length(parcel_to_list));
0018 
0019 % Set input files
0020 dmri_file        = fullfile(root, '/dmri/connectivity/connectivity.dmri.mat');
0021 parcel_dir       = fullfile(root, '/dmri/parcels');
0022 mif_file         = fullfile(root, '/dmri/fibertrack/CSD6.mif');
0023 mask_file        = fullfile(root, '/dmri/fibertrack/parcel_wm.nii.gz');
0024 fa_gz_file       = fullfile(root, '/dmri/DWI/data_FA.nii.gz');
0025 trans_info_dir   = fullfile(root, '/dmri/transwarp_info');
0026 fs_brain_gz_file = fullfile(root, '/freesurfer/Subject/mri/brain.nii.gz');
0027 
0028 
0029 % Output directory(filename is fixed : Vmni_connect.mat)
0030 output_dir       = '~/dynamics_movie';
0031 
0032 % Fiber tracking hosts(Do not specify a host that runs this script.)
0033 % Available hosts
0034 % - cbi-node20-33
0035 % - cbi-node01g-08g
0036 % - cbi-node20g-23g
0037 process_host     = {'cbi-node01g', 'cbi-node02g','cbi-node03g'};
0038 
0039 % The number of MATLAB processes which are used to process fiber tracking result files.
0040 Nworker          = 20;
0041 
0042 dmri_fiber_track_prob_specific_pair(parcel_dir, parcel_from_list, parcel_to_list, ...
0043                               mif_file, mask_file, ...
0044                               fa_gz_file, fs_brain_gz_file, trans_info_dir, dmri_file, ...
0045                               output_dir, process_host, Nworker);