convert_LOG_BIDS.m

function convert_LOG_BIDS(BIDS, biomax_table)
%
% copies the logfiles into BIDS format
%
% Required fields of convert_LOG_BIDS:
%
% file history:
% created M. Czisch & F. Binder 8.11.2017
% last M. Czisch 31.1.2018

cmd_str = sprintf('date >> %s/func/logfile_log_conversion.txt', BIDS.output.dir);
system(cmd_str);

cd([BIDS.input.dir]);
cd('LOG');

% check sanity
% TBD

% create correct file name
PatientID = BIDS.input.data_dir(1).PatientID{3};
tmp = strfind(PatientID,'FOR');
if tmp
    short_ID = 'F';
else
    short_ID = PatientID(3);
end
tmp     = str2num(PatientID(4:7));  % removes leading zeros
tmp_str = num2str(tmp);

short_ID = [short_ID, tmp_str];
filenames = dir([short_ID, '*.log']);
max = size(filenames,1);

% loop over all possible log files

for i=1:max
    
    
    clear cmd_str;
    
    log_str = [short_ID,'-Hariri.log'];
    if strcmp(filenames(i).name,log_str) & biomax_table{{'faces'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_task-hariri_bold.log',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str);
    end
    
    log_str = [short_ID,'-TET.log'];
    if strcmp(filenames(i).name,log_str) & biomax_table{{'TET'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_task-tet_bold.log',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str);
    end
    
    log_str = [short_ID,'-Nback.log'];
    if strcmp(filenames(i).name,log_str) & biomax_table{{'nback'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_task-nback_bold.log',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str);
    end
    
    log_str = [short_ID,'-reward.log'];
    if strcmp(filenames(i).name,log_str) & biomax_table{{'Reward'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_task-reward_bold.log',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str);
    end
    
    log_str = [short_ID,'-IST_final_122014.log'];   %these are the IST which were run with the HDMI box
    if strcmp(filenames(i).name,log_str) & biomax_table{{'IST'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_task-ist_bold.log',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str);
    end
    
    log_str = [short_ID,'-IST_flipped2.log'];       %these are the current IST 
    if strcmp(filenames(i).name,log_str) & biomax_table{{'IST'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_task-ist_bold.log',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str);
    end
    
    if exist('cmd_str')
        logfilename = sprintf('%s/func/logfile_log_conversion.txt', BIDS.output.dir);
        fid = fopen(logfilename,'a');
        fprintf(fid,'%s\n',cmd_str);
        fclose(fid);
    end
end

cd([BIDS.input.dir]);