dmri_label_file_to_FA_volume

 Create Parcel volume files on FA coordinate system from label 
 files(on FreeSurfer coordinate system).

 [Usage]
    dmri_label_file_to_FA_volume(label_dir, ...
                                 fs_dir, ref_struct_niigz_file, ...
                                 re_FA_niigz_file, trans_info_dir, ...
                                 output_dir, Npararel, mode)
 
 [Input]
                label_dir : The directory which contains parcel label files.
                   fs_dir : Freesurfer directory.
    ref_struct_niigz_file : reference structure image file (niftigz format).
        ref_FA_niigz_file : reference FA(Fractional anisotrophy) image file (niftigz format).
           trans_info_dir : The directory which cnotains transform infomation files
                            created by dti_transwarp_info_create.m
               output_dir : Parcels volume files will put into here.
                 Nprocess : [Optional]The number of processes that 
                                      want to use this conversion. Default = 4
                     mode : [Optional] Processsing mode
                              default  = 0 : Do all the operation(1-3)
                                       = 1 : Parcel label to Parcel FA volume files.
                                       = 2 : Parcel FA Volume files join to parcel_all.nii.gz
                                             and parcel_mm_coord MAT-file.
                                       = 3 : Create Parcel FA volumes exception files.

 [Output]
    none

 [Output files]
    N:Number of parcel files.

    Volume files:
        output_dir/parcel1.nii.gz to parcelN.nii.gz
        output_dir/parcel_all.nii.gz
        output_dir/parcel_ex1.nii.gz to parcel_exN.nii.gz

     * parcel_ex1.nii.gz = pacel_all.nii.gz - parcel1.nii.gz

    MAT-file:
        output_dir/parcel_mm_coord.mat
    Transform matrix file:
        output_dir/qform % from FreeSurfer coord to FA mm coord.


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

0001 function dmri_label_file_to_FA_volume(label_dir, ...
0002                                       fs_dir, ref_struct_niigz_file, ...
0003                                       ref_FA_niigz_file, trans_info_dir, ...
0004                                       output_dir, Nprocess, mode)
0005 % Create Parcel volume files on FA coordinate system from label
0006 % files(on FreeSurfer coordinate system).
0007 %
0008 % [Usage]
0009 %    dmri_label_file_to_FA_volume(label_dir, ...
0010 %                                 fs_dir, ref_struct_niigz_file, ...
0011 %                                 re_FA_niigz_file, trans_info_dir, ...
0012 %                                 output_dir, Npararel, mode)
0013 %
0014 % [Input]
0015 %                label_dir : The directory which contains parcel label files.
0016 %                   fs_dir : Freesurfer directory.
0017 %    ref_struct_niigz_file : reference structure image file (niftigz format).
0018 %        ref_FA_niigz_file : reference FA(Fractional anisotrophy) image file (niftigz format).
0019 %           trans_info_dir : The directory which cnotains transform infomation files
0020 %                            created by dti_transwarp_info_create.m
0021 %               output_dir : Parcels volume files will put into here.
0022 %                 Nprocess : [Optional]The number of processes that
0023 %                                      want to use this conversion. Default = 4
0024 %                     mode : [Optional] Processsing mode
0025 %                              default  = 0 : Do all the operation(1-3)
0026 %                                       = 1 : Parcel label to Parcel FA volume files.
0027 %                                       = 2 : Parcel FA Volume files join to parcel_all.nii.gz
0028 %                                             and parcel_mm_coord MAT-file.
0029 %                                       = 3 : Create Parcel FA volumes exception files.
0030 %
0031 % [Output]
0032 %    none
0033 %
0034 % [Output files]
0035 %    N:Number of parcel files.
0036 %
0037 %    Volume files:
0038 %        output_dir/parcel1.nii.gz to parcelN.nii.gz
0039 %        output_dir/parcel_all.nii.gz
0040 %        output_dir/parcel_ex1.nii.gz to parcel_exN.nii.gz
0041 %
0042 %     * parcel_ex1.nii.gz = pacel_all.nii.gz - parcel1.nii.gz
0043 %
0044 %    MAT-file:
0045 %        output_dir/parcel_mm_coord.mat
0046 %    Transform matrix file:
0047 %        output_dir/qform % from FreeSurfer coord to FA mm coord.
0048 %
0049 %
0050 % Copyright (C) 2011, ATR All Rights Reserved.
0051 % License : New BSD License(see VBMEG_LICENSE.txt)
0052 
0053 %
0054 % --- Previous check
0055 %
0056 if nargin < 6
0057     error('Please check input arguments.');
0058 end
0059 if ~exist('Nprocess', 'var')
0060     Nprocess = 2;
0061 end
0062 if exist(output_dir, 'dir') ~= 7
0063     mkdir(output_dir);
0064 end
0065 if ~exist('mode', 'var')
0066     mode = 0;
0067 end
0068 
0069 %
0070 % --- Main Procedure
0071 %
0072 
0073 process_list   = cell(0);
0074 start = tic;
0075 
0076 % Define terminate function
0077 function terminate_fcn
0078     % Kill fiber tracking process on specified hosts
0079     for k=1:length(process_list)
0080         process_list{k}.destroy();
0081     end
0082 end
0083 
0084 label_files    = dir([label_dir, filesep, 'parcel*.label']);
0085 Nfiles         = length(label_files);
0086 Nfile_per_proc = ceil(Nfiles / Nprocess);
0087 work_dir       = tempname(output_dir);
0088 mkdir(work_dir);
0089 
0090 if mode == 0 || mode == 1
0091 d = dir(fullfile(output_dir, filesep, 'parcel*.nii.gz'));
0092 Nexist = length(d);
0093 if Nexist ~= 0
0094     warning('Parcellation volume files are already exist. overwrite them.');
0095     delete(fullfile(output_dir, filesep, 'parcel*.nii.gz'));
0096     delete(fullfile(output_dir, filesep, 'parcel*.asc'));
0097     delete(fullfile(output_dir, filesep, 'qform'));
0098 end
0099 
0100 %%%%%%%%%%%%%%%%%%%%%%%%%%
0101 % label to FA volume
0102 %%%%%%%%%%%%%%%%%%%%%%%%%%
0103 fprintf('Creating Parcel volume files from Parcel label files.\n');
0104 files      = cell(0, 1);
0105 fids       = cell(0, 1);
0106 for k=1:Nfiles
0107     if mod(k, Nfile_per_proc) == 1
0108         Nth_script_file = length(files)+1;
0109         script_file     = fullfile(work_dir, filesep, ['script', num2str(Nth_script_file), '.sh']);
0110 
0111         % create template script
0112         isok = dmri_script_file_create(script_file);
0113         if isok == false, error('Failed to create script.'); end
0114 
0115         % open append mode
0116         fid = fopen(script_file, 'a');
0117         if fid == -1
0118             error('File open failed. processing terminated.');
0119         end
0120         fids{Nth_script_file}  = fid;
0121         files{Nth_script_file} = script_file;
0122     end
0123 
0124     % write command
0125     
0126     % label -> fs volume
0127     fs_vol_file     = fullfile(work_dir, filesep, ['tmp1_' num2str(k), '.nii.gz']);
0128     fprintf(fid,   ['mri_label2vol', ...
0129                    ' --label ' fullfile(label_dir, filesep, ['parcel' num2str(k), '.label']), ...
0130                    ' --temp ' fs_dir, '/mri/brain.nii.gz', ...
0131                    ' --o ' fs_vol_file ' --identity >/dev/null 2>&1 \n']);
0132     % fs volume -> struct volume
0133     struct_vol_file = fullfile(work_dir, filesep, ['tmp0_' num2str(k), '.nii.gz']);
0134     cmd = dmri_image_transform_cmd_get(fs_vol_file, struct_vol_file, ref_struct_niigz_file, 'fs2struct', trans_info_dir);
0135     fprintf(fid, '%s\n', cmd);
0136     
0137     % struct volume -> FA volume
0138     fa_vol_file     = fullfile(work_dir, filesep, ['tmp2_' num2str(k), '.nii.gz']);
0139     cmd = dmri_image_transform_cmd_get(struct_vol_file, fa_vol_file, ref_FA_niigz_file, 'struct2fa_nointerp', trans_info_dir);
0140     fprintf(fid, '%s\n', cmd);
0141     
0142     % Binarize volume
0143     fa_bin_file     = fullfile(output_dir, filesep, ['parcel' num2str(k), '.nii.gz']);
0144     fprintf(fid, '%s\n', ['fslmaths', ...
0145                          ' ' fa_vol_file,  ...
0146                          ' -thr 0', ...
0147                          ' -bin ', fa_bin_file]);
0148 
0149     % Convert Volume to ascii
0150     fa_ascii_file   = fullfile(output_dir, filesep, ['parcel' num2str(k), '-v.asc']);
0151     fprintf(fid, '%s\n', ['fsl2ascii', ...
0152                           ' ', fa_bin_file, ...
0153                           ' ', fa_ascii_file]);
0154     
0155     % remove '00000' at the end of filename
0156     fprintf(fid, '%s\n', ['mv', ...
0157                           ' ', [fa_ascii_file, '00000'], ...
0158                           ' ', fa_ascii_file]);
0159                           
0160 end
0161 
0162 % close script files
0163 for k=1:length(fids), fclose(fids{k}); end
0164 
0165 
0166 % Register clean up function(onCleanup is MATLAB builtin function)
0167 onCleanup(@terminate_fcn);
0168 
0169 % script files execution
0170 runtime = java.lang.Runtime.getRuntime();
0171 for k=1:length(files)
0172     cmd = files{k};
0173     process_list{length(process_list)+1} = runtime.exec(cmd);
0174 end
0175 
0176 % polling output directory
0177 while(1)
0178     d = dir(fullfile(output_dir, filesep, 'parcel*.nii.gz'));
0179     Ncreated = length(d);
0180     fprintf('Now processing (%d/%d)\n', Ncreated, Nfiles);
0181     if Ncreated >= Nfiles
0182         disp('Done.');
0183         break;
0184     end
0185     pause(30);
0186 end
0187 end
0188 
0189 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0190 % All Parcel volumes in one volume
0191 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0192 if mode == 0 || mode == 2
0193 fprintf('All the Parcel volumes into single volume....');
0194 
0195 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0196 % Create qform
0197 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0198 qform_file = fullfile(output_dir, filesep, 'qform');
0199 cmd = ['fslorient -getqform ', fullfile(output_dir, filesep, 'parcel1.nii.gz'),...
0200       ' > ' qform_file];
0201 dmri_system(cmd);
0202 
0203 parcel_all_file = fullfile(output_dir, filesep, 'parcel_all.nii.gz');
0204 copyfile(fullfile(output_dir, filesep, 'parcel1.nii.gz'), parcel_all_file);
0205 for k=2:Nfiles
0206     % write command
0207     parcel_n_file = fullfile(output_dir, filesep, ['parcel' num2str(k), '.nii.gz']);
0208     dmri_add_images(parcel_all_file, parcel_n_file, parcel_all_file);
0209 end
0210 fprintf('Done.\n');
0211 end
0212 
0213 % Create parcel vertices in mm on FA coordinate.
0214 if mode == 0 || mode == 2
0215 disp('Converting parcels into FA coordinate vertices...');
0216 parcels_mm_file = fullfile(output_dir, filesep, 'parcel_mm_coord.mat');
0217 save_mask_coordinate(output_dir, qform_file, parcels_mm_file, ...
0218                      Nfiles, ref_FA_niigz_file);
0219 delete(fullfile(output_dir, filesep, 'parcel*.asc'));
0220 
0221 end
0222 
0223 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0224 % Create ParcelN Ex mask files
0225 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0226 if mode == 0 || mode == 3
0227 fprintf('Creating Parcel ex-mask volume files.\n');
0228 parcel_all_file = fullfile(output_dir, filesep, 'parcel_all.nii.gz');
0229 fids_ex_mask  = cell(0);
0230 files_ex_mask = cell(0);
0231 for k=1:Nfiles
0232     parcel_n_file    = fullfile(output_dir, filesep, ['parcel' num2str(k), '.nii.gz']);
0233     parcel_n_ex_file = fullfile(output_dir, filesep, ['parcel_ex' num2str(k), '.nii.gz']);
0234     if mod(k, Nfile_per_proc) == 1
0235         Nth_script_file = length(files_ex_mask)+1;
0236         script_file     = fullfile(work_dir, filesep, ['ex_mask_script', num2str(Nth_script_file), '.sh']);
0237 
0238         % create template script
0239         isok = dmri_script_file_create(script_file);
0240         if isok == false, error('Failed to create script.'); end
0241 
0242         % open append mode
0243         fid = fopen(script_file, 'a');
0244         if fid == -1
0245             error('File open failed. processing terminated.');
0246         end
0247         fids_ex_mask{Nth_script_file}  = fid;
0248         files_ex_mask{Nth_script_file} = script_file;
0249     end
0250     
0251     cmd = ['fslmaths ' parcel_all_file, ...
0252            ' -sub ',    parcel_n_file,   ...
0253            ' ',         parcel_n_ex_file];
0254     fprintf(fid, '%s\n', cmd);
0255 end
0256 
0257 % close script files
0258 for k=1:length(fids_ex_mask), fclose(fids_ex_mask{k}); end
0259 
0260 process_list = cell(0);
0261 
0262 % Register clean up function(onCleanup is MATLAB builtin function)
0263 onCleanup(@terminate_fcn);
0264 
0265 % script files execution
0266 for k=1:length(files_ex_mask)
0267     process_list{k} = runtime.exec(files_ex_mask{k});
0268 end
0269 
0270 % polling output directory
0271 while(1)
0272     d = dir(fullfile(output_dir, filesep, 'parcel_ex*.nii.gz'));
0273     Ncreated = length(d);
0274     fprintf('Now processing (%d/%d)\n', Ncreated, Nfiles);
0275     if Ncreated >= Nfiles
0276         disp('Done.');
0277         break;
0278     end
0279     pause(30);
0280 end
0281 end
0282 
0283 % delete working directory.
0284 rmdir(work_dir, 's')
0285 
0286 toc(start);
0287 
0288 end