OPTIMA_repair_convert_GE_dwi2_to_BIDS.m

function OPTIMA_repair_convert_GE_dwi2_to_BIDS(BIDS, biomax_table)
%
% performes dicom2niix for 2nd dwi experiment and saves data in BIDS format
%
% Required fields of convert_GE_BIDS:
%
% BIDS  -  BIDS structure
% biomax_table - biomax_out information in table format
%
%
% file history:
% created M. Czisch 5.5.2020
% last edited M. Czisch 12.5.2020
% adapted for OPTIMA 13.11.2020
%
% this script is needed since dicom2niix has problems with the manual
% stopping of dwi2, which causes the volumes to have weird slice numbers sometimes
%
% as it occured previously that a database recovery messes up the order of
% files, there is a check if the general structure of the subdirectory is
% OK
%
% the present script reads the number of slices in the dwi, and deleted all slices
% of the last incomplete volume before dcm2niix

test_flag = 0;
i = 1; % day 1


max_series = size(BIDS.input.data_dir(i).subdir,2); % number of series in day 1

for j = 3:max_series %ignore '.' and '..'
    
    if logical(strfind(BIDS.input.data_dir(i).SeriesDescription{j},'polar'))
        if biomax_table{{'Pepolar'},{'Ser'}}
            
            % changes 5.5.2020, as in OPTIMA
            % check number of dicom slices
            % and delete incomplete volumes
            
            cd(BIDS.input.data_dir(i).name);
            cd(BIDS.input.data_dir(i).subdir{j});
            
            if exist('saved_dwi2')   % obviously, the script had been run before
                tmp_files = dir('a*');
            else
                tmp_files = dir('i*');
            end
            
            % check if the dicom files are in the correct format
            % as after a database recovery, this might be corrupted
            
            
            for k=1:size(tmp_files,1)
                
                input_name = tmp_files(k).name;
                tmp = strsplit(input_name,'MRDC.');
                tmp_num(k) = str2num(tmp{2});
                tmp_num2(k) = k;
                
            end
            
            %check if dwi file format is correct
            
            n_slices = double(BIDS.input.data_dir(i).N_of_slices{j});
            
            if (max(tmp_num-tmp_num2) > (n_slices/2 -1)) || (min(tmp_num-tmp_num2) < - (n_slices/2 -1))
                
                fprintf('\nWARNING: directory looks as if database is corrupted!\n');
                fprintf('resorting performed\n\n');
                resort_flag = 1;
                
            else
                
                fprintf('\ndirectory looks normal!\n');
                fprintf('no action required\n\n');
                resort_flag = 0;
                
            end
            
            if resort_flag
                
                [B,I]=sort(tmp_num);
                
                for k = 1:size(tmp_files,1)
                    
                    %output_name(k).name = tmp_files(I(k)).name;
                    counter = sprintf('%04d', k);
                    cmd_out = ['cp ',tmp_files(I(k)).name,' a', counter,'.MRDC.', num2str(k)];
                    system(cmd_out);
                    
                end
                cmd_out = ['mkdir saved_dwi2'];
                system(cmd_out);
                cmd_out = ['mv i* saved_dwi2'];
                system(cmd_out);
                tmp_str  = sprintf('a*MRDC.*');
            
            elseif ~resort_flag && size(dir('a*'),1)
                tmp_str  = sprintf('a*MRDC.*');
            else
                tmp_str  = sprintf('i*MRDC*');
            end
            
            
            tmp = dir(tmp_str);
            n_images = size(tmp,1);
            
            full_images = fix(n_images/n_slices);
            for b = (full_images*n_slices)+1:n_images
                cmd_str = ['rm ', tmp(b).name];
                system(cmd_str);
            end
            
            % make sure that directory only contains the dicom files
            
            cmd_out = ['mv saved_dwi2 ..'];
            system(cmd_out);
            
            
            cmd_str0 = ['repair_BIDS_1_0_2_dwi2.m run on ',date];
            cmd_str0 = sprintf('echo ''%s'' >> %s/dwi/logfile_%s_dwi_dcm2nii.txt', cmd_str0, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3})
            fprintf('\n%s', cmd_str0);
            
            if resort_flag
                cmd_str = sprintf('dcm2niix -f sub-%s_run-2_dwi -z y -o %s/dwi . >> %s/dwi/logfile_%s_dwi_dcm2nii.txt',...
                    BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
            else
                cmd_str = sprintf('dcm2niix -f sub-%s_run-2_dwi -z y -o %s/dwi . >> %s/dwi/logfile_%s_dwi_dcm2nii.txt',...
                    BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
            end
            
            fprintf('\n%s', cmd_str);
            if ~test_flag
                
                system(['rm ', BIDS.output.dir,'/dwi/*run-2_dwi*']);
                system(cmd_str0);
                system(cmd_str);
                cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_run-2_dwi.dicom.1 >> %s/dwi/logfile_%s_dwi_dcm2nii.txt', ...
                    BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
                system(cmd_str);
            end
            
            % and bring back the original backuped files
            cmd_out = ['mv ../saved_dwi2 .'];
            system(cmd_out);
            
        end
    end
end