Hariri_logfile_bids.m

% Hariri Logfile Extraction / Number of scans
%
% transfers logfiles into BIDS tsv format
%
% file history:
% created A. Kuehnel 18.12.2017
% last edited M. Czisch 31.1.2018


function Hariri_logfile_bids(BIDS)

subject_path = BIDS.output.dir;
log = dir([BIDS.output.dir,'/func/*hariri_bold.log']);
logfile=readtext([BIDS.output.dir,'/func/',log.name],'\t');
dummies = 0; %number of dummies

% Find last row with relevant information
last_row=find(strcmp(logfile(:,1),'Event Type'))-3;

% Convert to table

logfile_table = cell2table(logfile(6:last_row,1:8));
Var_Names = strrep(logfile(4,1:8),' ','');
logfile_table.Properties.VariableNames = Var_Names;

% Count Pulses (only if number pulses > nr. events && responses)

logfile_table.EventType=categorical(logfile_table.EventType);


% Find zerotime 

logfile_table.Time=logfile_table.Time/10000;
Pulse_index = strcmp(cellstr(logfile_table.EventType),'Pulse');
Response_index = find(strcmp(cellstr(logfile_table.EventType),'Response'));
Dummy_index = find(Pulse_index,dummies+1,'first');
zero_time = logfile_table.Time(Dummy_index(end));

% Find Indexes for different event types

temp = cellfun(@num2str, logfile_table.Code, 'UniformOutput', false);
Ende_index = ~cellfun(@isempty,(regexp(temp,'instruction2')));

if sum(Ende_index)==0; error('Incomplete Logfile!'); end

Jpeg_index = find(~cellfun(@isempty,(regexp(temp,'.jpg$'))));
Fix_index = find(~cellfun(@isempty,(regexp(temp,'fix_*'))));
Fix1_index = find(~cellfun(@isempty,(regexp(temp,'fix_cross1.jpg'))));
Fix2_index = find(~cellfun(@isempty,(regexp(temp,'fix_cross2.jpg'))));
Geo_index = find(~cellfun(@isempty,(regexp(temp,'e*'))));
Faces_index = setxor((setxor(Jpeg_index, Fix_index)),Geo_index);% Alternatively regexp pattern = '^[^ef]\w*\.jpg'
All_events_index = sort([Jpeg_index; Response_index]);

% Categorize Events % 1 fix1 2 fix2 3form 4face 5response/motor
logfile_table.cat=zeros(size(temp));
logfile_table.cat(Fix1_index)=1;
logfile_table.cat(Fix2_index)=2;
logfile_table.cat(Geo_index)=3;
logfile_table.cat(Faces_index)=4;
logfile_table.cat(Response_index)=5;


logfile_table.event=string(nan(size(temp)));
logfile_table.event(Fix1_index)='Fix1';
logfile_table.event(Fix2_index)='Fix2';
logfile_table.event(Geo_index)='Form';
logfile_table.event(Faces_index)='Face';
logfile_table.event(Response_index)='Motor';


% tsv/csv file for bids
% without Pulses 
event_durations = nan(length(All_events_index),1);
jpeg_durations = cell2mat(logfile_table.Duration(Jpeg_index))/10000;

%Calculate RTS as difference between begin stimulus presentaion and begin
%next event (Response or next fixation)
RT = nan(length(All_events_index),1);
[~,ai,~]=intersect(All_events_index,Jpeg_index);
RTs = [diff(logfile_table.Time(All_events_index));0];

event_onsets = logfile_table.Time(All_events_index)-zero_time;
stimulus = cellfun(@num2str, logfile_table.Code(All_events_index), 'UniformOutput', false);
event_cat = logfile_table.cat(All_events_index);
event_type = logfile_table.event(All_events_index);
event_durations(ai) = jpeg_durations;
RT(event_cat==3|event_cat==4) = RTs(event_cat==3 | event_cat==4);

% RT = NaN for RTs longer than presentation of stimulus
RT((event_cat==3&RTs>4)|(event_cat==4&RTs>6))=NaN;

log_tab=table(event_type,event_onsets,event_durations,RT,event_cat,stimulus);
%writetable(log, [subject_path,'/func/sub-',subject_path(end-6:end),'_task-hariri_events.csv'],'Delimiter','\t');

log_cell=[log_tab.Properties.VariableNames;table2cell(log_tab)];
fid = fopen([subject_path,'/func/sub-',subject_path(end-11:end-5),'_task-hariri_events.tsv'],'wt');
 if fid>0
     fprintf(fid, '%s\t%s\t%s\t%s\t%s\t%s\n',log_cell{1,:});
     for k=2:size(log_cell,1)
         fprintf(fid,'%s\t%f\t%f\t%f\t%f\t%s\n',log_cell{k,:});
     end
     fclose(fid);
 end