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abcd_extract_eprime_sst.m
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abcd_extract_eprime_sst.m
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function [eprime_nruns,eprime_runs,errcode,behav,errmsg] = abcd_extract_eprime_sst(fname,varargin)
%function [eprime_nruns,eprime_runs,errcode,behav,errmsg] = abcd_extract_eprime_sst(fname,[options])
%
% Purpose: extract condition time courses
% from eprime data files for SST task
%
% Required input:
% fname: name of input eprime file
%
% Optional input:
% 'outdir': output directory
% {default = pwd}
% 'outstem': output file stem
% if empty, will use filestem of fname
% {default = []}
% 'TR': scan repetition time (s)
% {default = 0.8}
% 'numTRs': number of repetitions
% {default = 500}
% 'minfrac': minimum fraction of a TR to register an event
% {default = 0.5}
% 'nskipTRs': number of TRs to remove from beginning of time course
% {default = 0}
% 'switch_thresh': percent correct below which to swap button assignements
% {default = 0.3}
% 'forceflag': [0|1] overwrite existing output
% {default = 0}
% 'timing_files_flag': [0|1] generate timing files
% {default = 1}
% 'verbose': [0|1] display messages
% {default = 1}
%
% Output:
% eprime_nruns: number of valid runs in the e-prime in the file
% errcode: [0|1] whether the file was successfully processed
% behav: behavioral data
% errmsg: string describing error if errcode=1
%
% Created: 10/07/16 by Don Hagler
% Prev Mod: 02/12/19 by Dani Cornejo
% Prev Mod: 03/12/19 by Feng Xue
% Prev Mod: 08/05/19 by Octavio Ruiz
% Prev Mod: 05/03/21 by Don Hagler
% Prev Mod: 08/31/21 by Don Hagler
% Prev Mod: 01/12/22 by Octavio Ruiz
% Prev Mod: 02/10/22 by Octavio Ruiz
% Prev Mod: 04/22/22 by Don Hagler
% Prev Mod: 06/14/24 by Don Hagler
% Last Mod: 06/25/24 by Don Hagler
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% NOTE: Based on make-SST-refs.py
% provided by Michael Michael Riedel, Ph.D. from FIU
% Using style from abcd_extract_eprime_mid.m
% provided by Donald J Hagler, Ph.D.
% Includes code for glitch and violator variables by Octavio Ruiz
% adapted from python code provided by Sage Hahn from UVM
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% initialize outputs
eprime_nruns = []; eprime_runs = []; errcode = 0; behav = []; errmsg = [];
% check arguments
if ~mmil_check_nargs(nargin,1), return; end;
% check input parameters
parms = check_input(fname,varargin);
% create output directory
mmil_mkdir(parms.outdir);
% create structure with info for each event
[event_info,start_time,all_types,errcode,errmsg] = get_event_info(parms);
if errcode, return; end;
% check for no responses
[nresp, errcode, errmsg] = check_no_responses(event_info,parms);
if errcode, return; end;
% switch buttons if necessary
% file _switched.csv will be created
[event_info,parms.switch_flag,errcode,errmsg] = sst_switch(event_info,parms);
if errcode, return; end;
%% todo: consolidate get_sst_types and write_event_revised?
% replace and/or add events names that were not coded
% correctly by E-prime
% e.g., late or early responses
all_types_new = get_sst_types(event_info,parms);
% write revised events (no changes in timing)
write_event_revised(parms,all_types_new);
% get behav data and write to csv file
% use revised events saved in all_types_new
[behav,eprime_runs,event_info,errcode,errmsg] = get_behavioral_data(event_info,parms,all_types_new);
if errcode, return; end;
parms.eprime_runs = eprime_runs;
eprime_nruns = length(eprime_runs);
parms.eprime_nruns = eprime_nruns;
if parms.verbose, fprintf('%s: number of e-prime runs = %d \n',mfilename,eprime_nruns); end
if parms.timing_files_flag && eprime_nruns
% create files for each condition
for i=1:parms.nconds
type = parms.typenames{i};
cond = parms.condnames{i};
pat = '\w_(?<event>\w+)';
k = regexp(cond,pat,'names');
eventname = k.event;
% use all_types_new, which is the revised information, to find all types of events
ind_type = find(strcmp(type,all_types_new));
% exclude extra events (e.g., partial run)
ind_type = intersect(ind_type,[1:length(event_info)]);
switch eventname
case 'go'
parms.mindur = 0.08;
% get onset
onset = {event_info(ind_type).('go_onset_time')};
% get offset
offset = {event_info(ind_type).('go_offset_time')};
% get resp_times
resp_times = {event_info(ind_type).('go_rt_adjusted')};
% check offsets match onsets
[onset,offset,resp_times] = check_offsets(onset,offset,resp_times,eventname,parms);
case 'stop'
parms.mindur = 0;
% get onset
onset = [event_info(ind_type).('stop_start_time')];
% set offset
offset = onset+20;
% get resp_times
resp_times = [event_info(ind_type).('stop_rt_adjusted')];
end
% find most recent start time for each event
[ind_start,event_ref_time] = set_ref(onset,start_time);
% create files for each scan
write_files(cond,onset,offset,resp_times,ind_start,event_ref_time,parms);
end
end; %timing_files_flag
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function parms = check_input(fname,options)
parms = mmil_args2parms(options,{...
'fname',fname,[],...
...
'outdir',pwd,[],...
'outstem',[],[],...
'TR',0.8,[],...
'numTRs',500,[],...
'minfrac',0.5,[0,1],...
'nskipTRs',0,[],...
'switch_thresh',0.3,[0,0.5],...
'forceflag',false,[false true],...
'timing_files_flag',true,[false true],...
'verbose',true,[false true],...
...
'eprime_runs',1:2,[],...
'eprime_nruns',0,0:2,...
'expected_numtrials',182,[],...
'expected_start_delay_GE',12,[],...
'expected_start_delay_Siemens',6.4,[],...
'expected_init_delay_GE',0,[],...
'expected_init_delay_Siemens',0,[],...
'start_delay_Siemens',6.4,[],...
'max_start_diff',0.5,[],...
'max_init_diff',5.0,[],...
...
'colnames', {'NARGUID','SessionDate','SessionTime','ExperimentName','ExperimentVersion',...
'Subject','Procedure[Block]','Block','Trial',...
'GetReady.RTTime','Wait4Scanner.RTTime','Wait4ScannerB.RTTime','BeginFix.StartTime','BeginFix.OnsetTime',...
'Go.RT', 'Fix.RT', 'StopSignal.RT','Go.Duration', 'SSDDur',...
'StopSignal.Duration','SSD.RT', 'Go.OnsetTime', 'Go.OffsetTime', 'Go.ACC' , 'Go.RESP',...
'Fix.RESP', 'SSD.OnsetTime','StopSignal.StartTime','SSD.OffsetTime','StopSignal.ACC', 'Go.CRESP',...
'StopSignal.RESP', 'SSD.ACC','TrialCode', 'SSD.RESP' },[],...
'fieldnames',{'narguid','date','time','experiment','version',...
'subject','procedure_block','block','trial',...
'getready_rttime','wait1_rttime','wait2_rttime','beginfix_st','beginfix_onset',...
'go_rt','fix_rt','stop_rt','go_dur','ssd_dur',...
'stop_dur','ssd_rt','go_onset_time','go_offset_time' , 'go_acc','go_resp',...
'fix_resp', 'ssd_onset_time','stop_start_time','ssd_offset_time','stop_acc','go_cresp',...
'stop_resp', 'ssd_acc', 'type', 'ssd_resp' },[],...
'typenames',{'CorrectGo', 'CorrectLateGo', 'IncorrectGo', 'IncorrectLateGo','NoRespGo',...
'CorrectStop', 'IncorrectStop','SSDStop'},[],...
'condnames',{'correct_go','correctlate_go', 'incorrect_go', 'incorrectlate_go' ...
'noresp_go', 'correct_stop', 'incorrect_stop','ssd_stop'},[],...
});
%% todo: option to specify which type(s) of file to write?
% check conditions
parms.nconds = length(parms.condnames);
parms.ntypes = length(parms.typenames);
parms.mindur = parms.minfrac*parms.TR;
if parms.nconds ~= parms.ntypes
error('condnames and typenames length mismatch');
end;
% check input file
if ~exist(parms.fname,'file')
error('file %s not found',parms.fname);
end;
[fdir,fstem,fext] = fileparts(parms.fname);
% remove problematic characters
if isempty(parms.outstem)
parms.outstem = abcd_clean_fstem(fstem);
end;
% compute time at the end of each TR
parms.TR_offset = linspace(parms.TR,parms.numTRs * parms.TR,parms.numTRs);
parms.TR_onset = parms.TR_offset - parms.TR;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [event_info,start_time,all_types,errcode,errmsg] = get_event_info(parms)
event_info=[]; start_time=[]; all_types=[];
errcode = 0; errmsg = [];
try
% write event info to file
fname_csv = abcd_check_eprime_sprdsh(parms.fname, parms.colnames,...
parms.fieldnames, parms.outdir, parms.outstem, parms.forceflag, parms.verbose);
event_info = mmil_csv2struct(fname_csv);
catch me
if parms.verbose
fprintf('%s: ERROR: failed to read or interpret e-prime file %s:\n%s\n',...
mfilename,parms.fname,me.message);
end
errcode = 1;
errmsg = 'failed to read or interpret e-prime file';
return;
end
% check experiment
experiment = mmil_getfield(event_info(1),'experiment');
if isempty(regexpi(experiment,'sst'))
if parms.verbose
fprintf('%s: ERROR: wrong experiment name in e-prime file %s: %s\n',...
mfilename,parms.fname,experiment);
end
errcode = 1;
errmsg = 'wrong experiment name';
return;
else
if parms.verbose, fprintf('%s: experiment name: %s\n',mfilename,experiment); end
end;
% check for behavioral or GE-specific experiment
behav_flag = 0; ge_flag = 0;
if ~isempty(regexpi(experiment,'behavioral'))
behav_flag = 1;
expected_start_delay = [0,0];
expected_init_delay = [0,0];
elseif ~isempty(regexp(experiment,'_GE'))
ge_flag = 1;
expected_start_delay = parms.expected_start_delay_GE*[1,1];
expected_init_delay = parms.expected_init_delay_GE*[1,1];
else
expected_start_delay = parms.expected_start_delay_Siemens*[1,1];
expected_init_delay = parms.expected_init_delay_Siemens*[1,1];
end
% get trigger and start times
trig_time = []; start_time = [];
if isfield(event_info,'getready_rttime') % GE
% get initial trigger times
ind_trig = find(~cellfun(@isempty,{event_info.getready_rttime}));
ind_trig_first = ind_trig(find([100,diff(ind_trig)]>1));
trig_time = [event_info(ind_trig_first).getready_rttime];
% exclude zeros
trig_time = nonzeros(trig_time)';
% NOTE: for GE, 16 triggers are sent/recorded
% set start_time to last trigger
ind_trig_last = ind_trig(find([diff(ind_trig),100]>1));
start_time = [event_info(ind_trig_last).getready_rttime];
% exclude zeros
start_time = nonzeros(start_time)';
elseif isfield(event_info,'wait1_rttime') || isfield(event_info,'wait2_rttime') % Siemens/Philips
% get initial trigger times
trig_time = [];
if isfield(event_info,'wait1_rttime')
ind_trig = find(~cellfun(@isempty,{event_info.wait1_rttime}));
if ~isempty(ind_trig)
trig_time = event_info(ind_trig(1)).wait1_rttime;
end
end
if isfield(event_info,'wait2_rttime')
ind_trig = find(~cellfun(@isempty,{event_info.wait2_rttime}));
if ~isempty(ind_trig)
trig_time = [trig_time,event_info(ind_trig(1)).wait2_rttime];
end
end
% exclude zeros
trig_time = nonzeros(trig_time)';
% set start time relative to trigger time
if behav_flag
% NOTE: for behavioral only, only one trigger is sent/recorded
% set start_time to trigger
start_time = trig_time;
else
% NOTE: for Siemens/Philips, only one trigger is sent/recorded
% set start_time relative to trigger with the standard start delay for Siemens/Philips
start_time = trig_time + 1000*parms.start_delay_Siemens;
end
end
% get init_time
ind_init = find(~cellfun(@isempty,{event_info.beginfix_onset}));
init_time = [event_info(ind_init).beginfix_onset];
% exclude zeros
init_time = nonzeros(init_time)';
% remove extra triggers
if length(trig_time) > length(init_time)
trig_time = trig_time(1:length(init_time));
end
% remove extra starts
if length(start_time) > length(init_time)
start_time = start_time(1:length(init_time));
end
if ge_flag
% check whether start delay diff is an integer multiple of TR
% indicating missed triggers
if length(start_time)==1
ex_start_delay = expected_start_delay(1);
else
ex_start_delay = expected_start_delay;
end
start_delay_diff = (start_time - trig_time) - 1000*ex_start_delay;
start_delay_diff_TR = start_delay_diff / (1000 * parms.TR);
start_delay_diff_TR_int = round(start_delay_diff_TR);
idx_miss = find(ismember(start_delay_diff_TR_int,[1:3]) & abs(start_delay_diff_TR - start_delay_diff_TR_int) <= 0.01);
if ~isempty(idx_miss)
if parms.verbose
for i=1:length(idx_miss)
fprintf('%s: WARNING: adjusting start_time for run %d by %0.2f seconds due to indications of missed triggers\n',...
mfilename,idx_miss(i),start_delay_diff(idx_miss(i))/1000);
end
end
% adjust start_time by subtracting start_delay_diff
start_time(idx_miss) = start_time(idx_miss) - start_delay_diff(idx_miss);
%% NOTE: start_time represents the start of the non-dummy imaging volume
%% init_time is when the stimulus starts
end
end
% check for disparity between trig_time and init_time
abcd_check_eprime_timing(trig_time,start_time,init_time,...
expected_start_delay,expected_init_delay,...
parms.outdir,parms.outstem,...
parms.max_start_diff,parms.max_init_diff,...
parms.verbose);
% remove non-events
all_types = {event_info.type};
ind_events = find(~cellfun(@isempty,all_types));
event_info = event_info(ind_events);
all_types = {event_info.type};
% check go_resp
go_resp = {event_info.go_resp};
fix_resp = {event_info.fix_resp};
stop_resp = {event_info.stop_resp};
go_cresp = {event_info.go_cresp};
if any(cellfun(@isstr,go_resp)) || any(cellfun(@iscell,go_resp)) ||...
any(cellfun(@isstr,fix_resp)) || any(cellfun(@iscell,fix_resp)) ||...
any(cellfun(@isstr,stop_resp)) || any(cellfun(@iscell,stop_resp))
if ~any(cellfun(@isstr,go_cresp))
if parms.verbose
fprintf('%s: ERROR: string go_resp values without string go_cresp values in e-prime file %s\n',...
mfilename,parms.fname);
end
errcode = 1;
errmsg = 'string go_resp values without string go_cresp values';
return;
end;
% get response numbers and names for unique, non-emptpy correct responses
uniq_go_cresp = unique(go_cresp(find(~cellfun(@isempty,go_cresp))));
num_cresp = length(uniq_go_cresp);
uniq_go_cresp_nums = [];
uniq_go_cresp_names = [];
for i=1:length(uniq_go_cresp)
% allow either '1{LEFTARROW}' or '1,{LEFTARROW}'
k = regexp(uniq_go_cresp{i},'(?<num>\d+),?{(?<name>\w+)}','names');
if ~isempty(k)
uniq_go_cresp_nums(i) = str2num(k.num);
uniq_go_cresp_names{i} = k.name;
else
% check for single character r, g, b, or y
k = regexp(uniq_go_cresp{i},'^(?<char>[rgby])$','names');
if ~isempty(k)
uniq_go_cresp_nums(i) = i;
uniq_go_cresp_names{i} = k.char;
else
if parms.verbose
fprintf('%s: ERROR: string go_cresp with unexpected pattern (%s) in e-prime file %s\n',...
mfilename,uniq_go_cresp{i},parms.fname);
end
errcode = 1;
errmsg = sprintf('string go_cresp with unexpected pattern (%s)',uniq_go_cresp{i});
return;
end;
end
end;
if parms.verbose
if parms.verbose
fprintf('%s: WARNING: replacing go_resp strings with numeric\n', mfilename);
end
end;
for i=1:length(event_info)
% assign numbers to each go_resp
go_resp = event_info(i).go_resp;
if iscell(go_resp), go_resp = go_resp{1}; end;
if isstr(go_resp)
k = find(strcmp(go_resp,uniq_go_cresp_names));
go_resp = uniq_go_cresp_nums(k);
end;
event_info(i).go_resp = go_resp;
% assign numbers to each fix_resp
fix_resp = event_info(i).fix_resp;
if iscell(fix_resp), fix_resp = fix_resp{1}; end;
if isstr(fix_resp)
k = find(strcmp(fix_resp,uniq_go_cresp_names));
fix_resp = uniq_go_cresp_nums(k);
end;
event_info(i).fix_resp = fix_resp;
% assign numbers to each stop_resp
stop_resp = event_info(i).stop_resp;
if iscell(stop_resp), stop_resp = stop_resp{1}; end;
if isstr(stop_resp)
k = find(strcmp(stop_resp,uniq_go_cresp_names));
stop_resp = uniq_go_cresp_nums(k);
end;
event_info(i).stop_resp = stop_resp;
% assign numbers to each ssd_resp
ssd_resp = event_info(i).ssd_resp;
if iscell(ssd_resp), ssd_resp = ssd_resp{1}; end;
if isstr(ssd_resp)
k = find(strcmp(ssd_resp,uniq_go_cresp_names));
ssd_resp = uniq_go_cresp_nums(k);
end;
event_info(i).ssd_resp = ssd_resp;
end;
end;
% check go_cresp
if any(cellfun(@isstr,{event_info.go_cresp}))
if parms.verbose
fprintf('%s: WARNING: replacing go_cresp strings with numeric\n', mfilename);
end
for i=1:length(event_info)
if isstr(event_info(i).go_cresp)
% remove text description of response
% allow either '1{LEFTARROW}' or '1,{LEFTARROW}'
event_info(i).go_cresp = str2num(regexprep(event_info(i).go_cresp,'[,{].+',''));
end;
end;
end;
% reset variables indicating accurate responses
event_info = sst_acc(event_info);
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% check for no responses
function [nresp, errcode, errmsg] = check_no_responses(event_info,parms)
nresp = 0; errcode = 0; errmsg = [];
% check go_resp, fix_resp, and stop_resp
go_resp = {event_info.go_resp};
fix_resp = {event_info.fix_resp};
stop_resp = {event_info.stop_resp};
ssd_resp = {event_info.ssd_resp};
% count number of responses (any type)
nresp = nnz(~cellfun(@isempty,go_resp)) +...
nnz(~cellfun(@isempty,fix_resp)) +...
nnz(~cellfun(@isempty,stop_resp)) +...
nnz(~cellfun(@isempty,ssd_resp));
% if no responses, set errcode and errmsg
if nresp == 0
if parms.verbose, fprintf('%s: ERROR: no responses in %s\n',mfilename,parms.fname); end
errcode = 1;
errmsg = 'no responses';
return;
end
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function event_info = sst_acc(event_info)
for i=1:length(event_info)
if event_info(i).go_resp == event_info(i).go_cresp
event_info(i).go_acc=1;
elseif event_info(i).go_resp ~= event_info(i).go_cresp
event_info(i).go_acc=0;
end
end
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [event_info,switch_flag,errcode,errmsg] = sst_switch(event_info,parms)
[switch_flag,acc1,errcode,errmsg] = sst_switch_flag(event_info,parms);
if errcode, return; end;
if switch_flag
event_info = sst_switch_event(event_info);
[~,acc2,~] = sst_switch_flag(event_info,parms);
if acc2 < acc1
event_info = sst_switch_event(event_info);
switch_flag = 0;
end
end
% write to csv
if switch_flag
fname_csv_out = sprintf('%s/%s_events_switched.csv',...
parms.outdir,parms.outstem);
if ~exist(fname_csv_out,'file') || parms.forceflag
mmil_struct2csv(event_info,fname_csv_out)
end;
end;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function event_info = sst_switch_event(event_info)
for i=1:length(event_info)
event_info(i).go_resp = switch_val(event_info(i).go_resp);
event_info(i).fix_resp = switch_val(event_info(i).fix_resp);
event_info(i).stop_resp = switch_val(event_info(i).stop_resp);
event_info(i).ssd_resp = switch_val(event_info(i).ssd_resp);
end
event_info = sst_acc(event_info);
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function val = switch_val(val)
if val==1
val=2;
elseif val==2
val=1;
end;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [switch_flag,accuracy,errcode,errmsg] = sst_switch_flag(event_info,parms)
switch_flag = 0;
errcode = 0; errmsg = [];
all_types = [event_info.go_acc];
correct_total = size(all_types,2);
correct = sum(all_types);
accuracy = 100*correct/correct_total;
if parms.verbose, fprintf('%s: accuracy = %0.1f%%\n',mfilename,accuracy); end
if accuracy < 100*parms.switch_thresh
if parms.verbose, fprintf('%s: accuracy < %0.1f%%, switching button responses\n',...
mfilename,100*parms.switch_thresh); end
switch_flag = 1;
end;
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% todo: consolidate get_sst_types and write_event_revised?
function write_event_revised(parms,all_types_new)
% purpose: Replace and/or add events names that were not coded
% correctly by the e-prime software and write to a csv file.
% all_types_new already has this informantion computed by
% get_sst_types().
% output file name
if parms.switch_flag
fname_csv_in = sprintf('%s/%s_events_switched.csv',parms.outdir,parms.outstem);
else
fname_csv_in = sprintf('%s/%s_events.csv',parms.outdir,parms.outstem);
end;
fname_csv_out = sprintf('%s/%s_events_revised.csv',parms.outdir,parms.outstem);
% output file writing
if ~exist(fname_csv_out,'file') || parms.forceflag
% event info
event_info = mmil_csv2struct(fname_csv_in);
% find events
all_types = {event_info.type};
ind_events = find(~cellfun(@isempty,all_types));
for i=1:length(ind_events)
event_info(ind_events(i)).type = char(all_types_new(i));
end
% write to csv
if ~exist(fname_csv_out,'file') || parms.forceflag
mmil_struct2csv(event_info,fname_csv_out);
end;
end;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% todo: return event_info with new types?
function all_types_new = get_sst_types(event_info,parms)
all_types_new = {event_info.type};
% correct_go
go_cresp = {event_info.go_cresp};
go_resp = {event_info.go_resp};
correct_go_ind = [];
for i=1:size(go_cresp,2)
if go_resp{i} == go_cresp{i}
correct_go_ind = [correct_go_ind i];
all_types_new{i} = 'CorrectGo';
end
end
% correct_go_late
fix_resp = {event_info.fix_resp};
correct_go_late_ind = [];
for i=1:size(go_cresp,2)
if fix_resp{i} == go_cresp{i}
if go_resp{i} == go_cresp{i}
else
correct_go_late_ind = [correct_go_late_ind i];
all_types_new{i} = 'CorrectLateGo';
end
end
end
% no_resp_go
go_event_ind = find(~cellfun(@isempty,go_cresp));
noresp_ind = find(cellfun(@isempty,go_resp));
nofix_ind = find(cellfun(@isempty,fix_resp));
noresp_nofix_ind = [intersect(noresp_ind,nofix_ind)];
no_resp_go_ind = [intersect(noresp_nofix_ind,go_event_ind)];
for i=no_resp_go_ind
all_types_new{i} = 'NoRespGo';
end
% incorrect_go
incorrect_go_ind = [];
incorrect_go_late_ind = [];
for i=1:size(go_cresp,2)
if go_resp{i} ~= go_cresp{i}
incorrect_go_ind = [incorrect_go_ind i];
all_types_new{i} = 'IncorrectGo'; %legit 1~=2
elseif go_resp{i} == go_cresp{i}
else
if fix_resp{i} ~= go_cresp{i}
incorrect_go_late_ind = [incorrect_go_late_ind i];
all_types_new{i} = 'IncorrectLateGo';
end
end
end
% correct & incorrect _stop
ssd_rt = {event_info.ssd_rt};
ssd_dur = {event_info.ssd_dur};
stop_resp = {event_info.stop_resp};
fix_resp = {event_info.fix_resp};
incorrect_stop_ind = [];
correct_stop_ind = [];
ssd_stop_ind = [];
for i=1:size(ssd_dur,2)
if ssd_dur{i} > 0 % only stop trials
if stop_resp{i} > 0
incorrect_stop_ind = [incorrect_stop_ind i];
all_types_new{i} = 'IncorrectStop';
elseif fix_resp{i} > 0
incorrect_stop_ind = [incorrect_stop_ind i];
all_types_new{i} = 'IncorrectStop';
else
correct_stop_ind = [correct_stop_ind i];
all_types_new{i} = 'CorrectStop';
end
if ssd_rt{i} > 0
% stop too early
ssd_stop_ind = [ssd_stop_ind i];
all_types_new{i} = 'SSDStop';
end
end
end
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ind_start,event_ref_time] = set_ref(onset,start_time)
if ~isempty(onset)
d = bsxfun(@minus,onset,start_time');
d(d<0) = Inf;
[d,ind_start] = min(d,[],1);
event_ref_time = start_time(ind_start);
else
ind_start = start_time;
event_ref_time = 0;
end;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [onset,offset,resp_times] = check_offsets(onset,offset,resp_times,eventname,parms)
ind_empty = find(cellfun(@isempty,onset) | cellfun(@isempty,offset));
if ~isempty(ind_empty)
if parms.verbose
fprintf('%s: WARNING: %s event has %d onsets and %d offsets\n',...
mfilename,eventname,nnz(~cellfun(@isempty,onset)),nnz(~cellfun(@isempty,offset)));
% NOTE: this may indicate file truncation
end
ind_keep = setdiff([1:length(onset)],ind_empty);
onset = onset(ind_keep);
offset = offset(ind_keep);
resp_times = resp_times(ind_keep);
end;
onset = cell2mat(onset);
offset = cell2mat(offset);
if iscell(resp_times), resp_times = cell2mat(resp_times); end
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function write_files(eventname,onset,offset,resp_times,ind_start,event_ref_time,parms)
nscans = parms.eprime_nruns;
scans = parms.eprime_runs;
for s=scans
ind_scan = find(ind_start == s);
fname_1D = sprintf('%s/%s_scan%d_%s.1D',...
parms.outdir,parms.outstem,s,eventname);
fname_txt = sprintf('%s/%s_scan%d_%s.txt',...
parms.outdir,parms.outstem,s,eventname);
fname_block = sprintf('%s/%s_scan%d_%s_block.txt',...
parms.outdir,parms.outstem,s,eventname);
fname_block_dur = sprintf('%s/%s_scan%d_%s_block_dur.txt',...
parms.outdir,parms.outstem,s,eventname);
fname_fsl = sprintf('%s/%s_scan%d_%s_fsl.txt',...
parms.outdir,parms.outstem,s,eventname);
fname_rt = sprintf('%s/%s_scan%d_%s_rt.txt',...
parms.outdir,parms.outstem,s,eventname);
if ~exist(fname_1D,'file') || ~exist(fname_txt,'file') || ...
~exist(fname_block,'file') || ~exist(fname_fsl,'file') ||...
~exist(fname_rt,'file') || parms.forceflag
if ~isempty(onset(ind_scan))
% subtract start time and convert to seconds
rel_onset = (onset(ind_scan) - event_ref_time(ind_scan))/1000;
rel_offset = (offset(ind_scan) - event_ref_time(ind_scan))/1000;
% get resp_times for this scan
rel_resp_times = resp_times(ind_scan)/1000;
% loop over events
TR_mask = zeros(parms.numTRs,1);
for k=1:length(rel_onset)
ind_rep = find(rel_onset(k)<(parms.TR_offset-parms.mindur) &...
rel_offset(k)>(parms.TR_onset+parms.mindur));
TR_mask(ind_rep) = 1;
end;
% calculate event times from TR_onset
event_times = parms.TR_onset(find(TR_mask));
% convert time units to multiples of TRs
event_TRs = event_times/parms.TR;
% remove nskipTRs
if parms.nskipTRs>0
TR_mask = TR_mask(parms.nskipTRs+1:end);
event_times = event_times(parms.nskipTRs+1:end) - parms.nskipTRs*parms.TR;
event_TRs = event_times/parms.TR;
end;
% write to 1D file
fid = fopen(fname_1D,'wt');
if fid<0, error('failed to open %s for writing',fname_1D); end;
for k=1:length(TR_mask)
fprintf(fid,'%d\n',TR_mask(k));
end;
fclose(fid);
% write to txt file with stim times in seconds
fid = fopen(fname_txt,'wt');
if fid<0, error('failed to open %s for writing',fname_txt); end;
fprintf(fid,'%s\n',sprintf('%0.2f ',event_TRs*parms.TR));
fclose(fid);
% write to block txt file
fid = fopen(fname_block,'wt');
if fid<0, error('failed to open %s for writing',fname_block); end;
fprintf(fid,'%s\n',sprintf('%0.2f ',rel_onset));
fclose(fid);
fid = fopen(fname_block_dur,'wt');
if fid<0, error('failed to open %s for writing',fname_block_dur); end;
block_len = mean(rel_offset- rel_onset);
fprintf(fid,'%s\n',sprintf('%0.2f ',block_len));
fclose(fid);
% write to fsl file
fid = fopen(fname_fsl,'wt');
if fid<0, error('failed to open %s for writing',fname_fsl); end;
for i=1:length(rel_onset)
fprintf(fid, '%0.2f %0.2f 1 \n',rel_onset(i), rel_offset(i)-rel_onset(i));
end
fclose(fid);
% write to rt file
fid = fopen(fname_rt,'wt');
if fid<0, error('failed to open %s for writing',fname_rt); end;
for i=1:length(rel_resp_times)
fprintf(fid, '%0.3f\n',rel_resp_times(i));
end
fclose(fid);
else
TR_mask = zeros(parms.numTRs,1);
% write to 0s 1D file
fid = fopen(fname_1D,'wt');
if fid<0, error('failed to open %s for writing',fname_1D); end;
for k=1:length(TR_mask)
fprintf(fid,'%d\n',TR_mask(k));
end;
fclose(fid);
% write * txt file
fid = fopen(fname_txt,'wt');
if fid<0, error('failed to open %s for writing',fname_txt); end;
fprintf(fid,'*\n');
fclose(fid);
% write * txt file block
fid = fopen(fname_block,'wt');
if fid<0, error('failed to open %s for writing',fname_block); end;
fprintf(fid,'*\n');
fclose(fid);
fid = fopen(fname_block_dur,'wt');
if fid<0, error('failed to open %s for writing',fname_block); end;
fprintf(fid,'0\n');
fclose(fid);
% write empty fsl file
fid = fopen(fname_fsl,'wt');
if fid<0, error('failed to open %s for writing',fname_fsl); end;
fclose(fid);
% write empty rt file
fid = fopen(fname_rt,'wt');
if fid<0, error('failed to open %s for writing',fname_rt); end;
fclose(fid);
end
end;
end;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [behav,runs_ok,event_info,errcode,errmsg] = get_behavioral_data(event_info,parms,all_types_new)
errcode = 0; errmsg = [];
behav = [];
behav.('SubjID') = []; behav.('VisitID') = [];
behav.version = mmil_getfield(event_info(1),'version','UNKNOWN');
if parms.verbose
fprintf('%s: experiment version = %s\n',mfilename,behav.version);
end
behav.switch_flag = parms.switch_flag;
behav.perform_flag = 1;
blocks = [event_info.block];
trials = [event_info.trial];
% determine version of task
n_blocks = size(unique(blocks),2);
n_trials = size(unique(trials),2);
if n_trials > 2,
blocks = [event_info.block];
else
blocks = [event_info.trial];
end
% check if runs are truncated
runs = blocks;
nruns = length(unique(blocks));
runs_ok = [];
for i=1:nruns
run_len = length(find(runs==i));
if run_len == parms.expected_numtrials
runs_ok = [runs_ok i];
else
if parms.verbose
fprintf('%s: WARNING: run %d is short: %d trials found (expected %d)\n',...
mfilename,i,run_len,parms.expected_numtrials);
end
end
end
nruns = length(runs_ok);
if nruns == 1
ind_ok = find(runs==runs_ok);
all_types_new = all_types_new(ind_ok);
blocks = blocks(ind_ok);
event_info = event_info(ind_ok);
runs = runs(ind_ok);
elseif nruns == 0
if parms.verbose, fprintf('%s: ERROR: no valid e-prime runs in %s\n',mfilename,parms.fname); end
errcode = 1;
errmsg = 'no valid e-prime runs';
return;
end
behav.nruns = nruns;
% event durations
go_dur = {event_info.go_dur};
time_go_dur = [event_info.go_dur];
time_go_dur = time_go_dur(1);
stop_dur = {event_info.stop_dur};
go_event_ind = find(~cellfun(@isempty,go_dur));
stop_event_ind = find(~cellfun(@isempty,stop_dur));
% total numbers of trials
behav.('Go_total') = size(go_event_ind,2);
behav.('Stop_total') = size(stop_event_ind,2);
behav.('Total') = size(go_event_ind,2)+size(stop_event_ind,2);
% number of trials per run
for j=1:2 %runs
% go
type_counts_run_go = sprintf('Go_total_run_%d',j);
behav.(type_counts_run_go) = 'NaN';
% stop
type_counts_run_stop = sprintf('Stop_total_run_%d',j);
behav.(type_counts_run_stop) = 'NaN';
end
for j=runs_ok %runs
% go
type_counts_run_go = sprintf('Go_total_run_%d',j);
ind_type_run = [intersect(find(blocks==j),go_event_ind)];
behav.(type_counts_run_go) = size(ind_type_run,2);
% stop
type_counts_run_stop = sprintf('Stop_total_run_%d',j);
ind_type_run = [intersect(find(blocks==j),stop_event_ind)];
behav.(type_counts_run_stop) = size(ind_type_run,2);
end
% results for each condition
for i=1:parms.nconds
% total counts per type
type = parms.typenames{i};
type_counts_total = sprintf('%s_counts_total',type);
ind_type = find(strcmp(type,all_types_new));
behav.(type_counts_total) = size(ind_type,2);
% total counts per type per run
for j=1:2 % runs
type_counts_run = sprintf('%s_counts_run_%d',type,j);
behav.(type_counts_run) = 'NaN';
end
for j=runs_ok
type_counts_run = sprintf('%s_counts_run_%d',type,j);
ind_type_run = [intersect(find(blocks==j),ind_type)];
behav.(type_counts_run) = size(ind_type_run,2);
end
% selecting go or stop event
cond = parms.condnames{i};
pat = '\w_(?<event>\w+)';
k = regexp(cond,pat,'names');
eventname = k.event;
switch eventname
case 'go'
event_ind = go_event_ind;
event_rt = {event_info.('go_rt')};
if strcmp(cond,'correctlate_go')
event_rt_fix = {event_info.('fix_rt')};
event_rt = cellfun(@(x) x+time_go_dur, event_rt_fix,'UniformOutput',false);
end
if strcmp(cond,'incorrectlate_go')
event_rt_fix = {event_info.('fix_rt')};
event_rt = cellfun(@(x) x+time_go_dur, event_rt_fix,'UniformOutput',false);
end
case 'stop'
event_ind = stop_event_ind;
event_rt = {event_info.('stop_rt')};
end
% total percent per type
type_percent_total = sprintf('%s_percent_total',type);
behav.(type_percent_total) = size(ind_type,2)./size(event_ind,2);
% percent per type per run
for j=1:2 % runs
type_counts_run = sprintf('%s_percent_run_%d',type,j);
behav.(type_counts_run) = 'NaN';
end
for j=runs_ok
type_counts_run = sprintf('%s_percent_run_%d',type,j);
ind_type_run = [intersect(find(blocks==j),ind_type)];
ind_type_percent_run = [intersect(find(blocks==j),event_ind)];
behav.(type_counts_run) = size(ind_type_run,2)./size(ind_type_percent_run,2);
end
% total rt per type
type_rt_total = sprintf('%s_rt_total',type);
all_rt = cell2mat(event_rt(ind_type));
behav.(type_rt_total) = mean(all_rt(all_rt~=0));
type_rt_std_total = sprintf('%s_rt_std_total',type);
behav.(type_rt_std_total) = std(all_rt(all_rt~=0));
% total rt per type per run
for j=1:2 % runs
type_rt_runs = sprintf('%s_rt_run_%d',type,j);
behav.(type_rt_runs) = 'NaN';
type_rt_std_runs = sprintf('%s_rt_std_run_%d',type,j);
behav.(type_rt_std_runs) = 'NaN';
end
for j=runs_ok % runs
type_rt_runs = sprintf('%s_rt_run_%d',type,j);