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preproc_readMEG.m
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preproc_readMEG.m
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function [] = preproc_readMEG(sj)
% Read in and apply preprocessing to the data from one subject
% 1. read in continuous data, only the chans we need
% 2. downsample to 400 Hz
% 3. match eyelink files
% 4. epoch into trials
if ~isdeployed,
addpath(genpath('~/code/MEG'));
addpath(genpath('~/code/Tools'));
addpath('~/Documents/fieldtrip');
ft_defaults; warning off;
end
if ischar(sj), sj = str2double(sj); end
% ==================================================================
% LOAD IN SUBJECT SPECIFICS AND READ DATA
% ==================================================================
subjectdata = subjectspecifics(sj);
for session = 1:length(subjectdata.session),
disp(['Analysing subject ' num2str(sj) ', session ' num2str(session)]);
for rec = subjectdata.session(session).recsorder,
clearvars -except sj session subjectdata rec
if exist(sprintf('%s/P%02d-S%d_rec%d_data.mat', ...
subjectdata.preprocdir, sj, session, rec), 'file'),
% continue;
end
% ==================================================================
% READ IN CONTINUOUS DATA
% ==================================================================
% read in the dataset as a continuous segment
disp(subjectdata.session(session).rec(rec).dataset);
cfg = [];
cfg.dataset = sprintf('%s/%s', subjectdata.rawdir, ...
subjectdata.session(session).rec(rec).dataset);
cfg.continuous = 'yes'; % read in the data
cfg.precision = 'single'; % for speed and memory issues
cfg.sj = sj;
cfg.session = session;
cfg.rec = rec;
cfg.detrend = 'no';
cfg.demean = 'yes';
% preselect only those channels that are useful
% for testing, restrict the subset of MEG sensors
cfg.channel = {'M*', ...
'EEG001', 'EEG006', 'EEG012', 'EEG018', 'EEG024', 'EEG059', ...
'HLC*', 'UPPT*', 'UADC*'};
data = ft_preprocessing(cfg);
% ==================================================================
% RENAME AND REREF EEG CHANS
% ==================================================================
data.label = strrep(data.label, 'EEG001', 'EOGright');
data.label = strrep(data.label, 'EEG006', 'EOGleft');
data.label = strrep(data.label, 'EEG012', 'EOGtop');
data.label = strrep(data.label, 'EEG018', 'EOGbottom');
data.label = strrep(data.label, 'EEG024', 'POz');
data.label = strrep(data.label, 'EEG059', 'EKG');
data.label = strrep(data.label, 'UADC002', 'EYEH');
data.label = strrep(data.label, 'UADC003', 'EYEV');
data.label = strrep(data.label, 'UADC004', 'EYEPUPIL');
% rereference horizontal EOG chans
data.trial{1}(find(~cellfun(@isempty, strfind(data.label, 'EOGright'))), :) = ...
data.trial{1}(find(~cellfun(@isempty, strfind(data.label, 'EOGright'))), :) - ...
data.trial{1}(find(~cellfun(@isempty, strfind(data.label, 'EOGleft'))), :);
data.label = strrep(data.label, 'EOGright', 'EOGH'); % rename
% rereference vertical EOG chans
data.trial{1}(find(~cellfun(@isempty, strfind(data.label, 'EOGtop'))), :) = ...
data.trial{1}(find(~cellfun(@isempty, strfind(data.label, 'EOGtop'))), :) - ...
data.trial{1}(find(~cellfun(@isempty, strfind(data.label, 'EOGbottom'))), :);
data.label = strrep(data.label, 'EOGtop', 'EOGV'); % rename
% remove the chans we dont need anymore
cfg = [];
cfg.channel = {'all', '-EOGbottom', '-EOGleft'};
data = ft_preprocessing(cfg, data);
data = rmfield(data, 'cfg'); % keep it small
% ==================================================================
% DOWNSAMPLE
% ==================================================================
oldfs = 1200; % original sampling rate of all recordings
newfs = 400; % 1/3rd the MEG sampling rate, can still see up to 120 Hz gamma
assert(data.fsample == oldfs, 'MEG data not collected at 1200 Hz');
cfg = [];
cfg.resamplefs = newfs;
cfg.detrend = 'no'; % dont detrend if i want to look at cpp
cfg.demean = 'yes'; % will subtract the baseline = mean of all data
data = ft_resampledata(cfg, data);
% ==================================================================
% PARSE EVENTS
% ==================================================================
cfg = [];
cfg.dataset = sprintf('%s/%s', subjectdata.rawdir, ...
subjectdata.session(session).rec(rec).dataset);
cfg.trialfun = 'trialfun_allevents';
% workaround for the first recording day, not all
% triggers saved... load in from behav file
if ismember(sj, [2 3 4 5 27]) && session == 1,
cfg.trialfun = 'trialfun_allevents_retrievetimings';
end
cfg.trialdef.pre = 0.51; % before reference start (including fix)
cfg.trialdef.post = 2; % after feedback
cfg.sj = sj;
cfg.session = session;
cfg.rec = rec;
cfg = ft_definetrial(cfg); % define all trials
% check that this doesn't lead to overlapping trials
for t = 1:size(cfg.trl, 1)-1,
assert(cfg.trl(t, 2) < cfg.trl(t+1, 1), 'wrong');
end
% downsample the sample idx
newfs = 400;
samplerows = find(mean(cfg.trl) > 100);
cfg.trl(:,samplerows) = round(cfg.trl(:,samplerows) * (newfs/oldfs));
% add a unique idx at the end
% subject, session, block, trialnr
idx = sj * 1000000 + cfg.trl(:, 17) * 10000 ...
+ cfg.trl(:, 16) * 100 + cfg.trl(:, 15);
% make sure all idx are unique
assert(numel(unique(idx)) == length(idx), 'idx needs to be unique!');
cfg.trl(:, end+1) = idx;
% will use this to match EL and motionenergy
trialdefinition = cfg.trl;
% ==================================================================
% DO A CHECK ON THE BLOCK NRS
% ==================================================================
nrtrls = size(trialdefinition, 1);
nblocks = length(subjectdata.session(session).rec(rec).blocks);
% check if there are known missing trials from this dataset
missingtrials = [];
for b = subjectdata.session(session).rec(rec).blocks,
try % see if there are known missed trials
missingtrials = [missingtrials ...
subjectdata.session(session).rec(rec).block(b).missingtrials];
end
end
assert((nrtrls+length(missingtrials))/60 == nblocks, ...
'mistake in subjectspecifics');
% % ==================================================================
% % MATCH WITH EYELINK
% % ==================================================================
% recdate = regexp(subjectdata.session(session).rec(rec).dataset, '201\d*', 'match');
% recdate = datenum(recdate{1}, 'yyyymmdd');
% % when no eyelink was recorded, fill those chans with zeros
% if recdate < datenum('20140515', 'yyyymmdd') || ...
% (sj == 6 && session == 1) || ...
% (sj == 31 && session == 2 && rec == 2),
% % zeros may mess up the statistics!
% disp('No EyeLink recorded, filling with NaNs');
% eyechans = find(~cellfun(@isempty, strfind(data.label, 'EYE')));
% for e = 1:length(eyechans),
% data.trial{1}(eyechans(e), :) = nan(1, size(data.trial{1}, 2));
% end
% else
% % ==================================================================
% % GET DATA FROM EYELINK
% % ==================================================================
% % on 13-07-2015, we installed the analogue link so afterwards
% % the eyelink channels are already there
% if recdate < datenum('20150713', 'yyyymmdd'), replace = 1;
% else replace = 0; end
% for b = subjectdata.session(session).rec(rec).blocks,
% % get the right session nr
% if session == 2, thissession = 5;
% elseif session == 1, thissession = 1; end
% % convert edf to asc if needed
% ascFile = dir(sprintf('%s/EL_P%d_s%d_b%d_*.asc', subjectdata.eyedir, sj, thissession, b));
% if isempty(ascFile),
% edfFile = dir(sprintf('%s/EL_P%d_s%d_b%d_*.edf', subjectdata.eyedir, sj, thissession, b));
% edfFile = sprintf('%s/%s', subjectdata.eyedir, edfFile.name);
% system(sprintf('%s %s -input -failsafe', '~/code/Tools/eye/edf2asc-linux', edfFile)); % failsafe mode for corrupted edfs
% ascFile = dir(sprintf('%s/EL_P%d_s%d_b%d_*.asc', subjectdata.eyedir, sj, thissession, b));
% end
% % read in asc file from disk
% assert(length(ascFile) == 1);
% asc = read_eyelink_ascNK_AU([subjectdata.eyedir '/' ascFile.name]);
% % workaround for lost messages: retrieved from fixtime and ref timestamp
% if sj == 10 && session == 1 && b == 1,
% timestamp = round(15889758 - 0.6380*1000);
% asc.msg{77} = ['MSG ' num2str(timestamp) ' block1_trial6_fix'];
% elseif sj == 10 && session == 1 && b == 5,
% timestamp = round(19429421 - 0.8162*1000);
% asc.msg{37} = ['MSG ' num2str(timestamp) ' block5_trial1_fix'];
% elseif sj == 11 && session == 1 && b == 1,
% timestamp = round(2179361 - 0.8530*1000);
% asc.msg{57} = ['MSG ' num2str(timestamp) ' block1_trial4_fix'];
% elseif sj == 19 && session == 1 && b == 1,
% timestamp = round(10810223 - 0.5788*1000);
% asc.msg{45} = ['MSG ' num2str(timestamp) ' block1_trial2_fix'];
% end
% % match to MEG data
% cfg = [];
% cfg.sj = sj;
% cfg.session = session;
% cfg.rec = rec;
% cfg.block = b;
% data = pupil_syncEyeMEG(cfg, data, trialdefinition, asc, replace, 0);
% end
% % ==================================================================
% % show the resulting pupil signal for the whole recording
% % ==================================================================
% clf;
% xlimrange = linspace(data.time{1}(1), data.time{1}(end), ...
% length(subjectdata.session(session).rec(rec).blocks)+1);
% for sp = 1:length(xlimrange)-1,
% subplot(7,1,sp);
% plot(data.time{1}, (data.trial{1}(find(~cellfun(@isempty, ...
% strfind(lower(data.label), 'eyepupil'))), :)));
% % define range
% xlim([xlimrange(sp) xlimrange(sp+1)]);
% ylim([-4 4]); box off; % zscored, so plot plausible range
% set(gca, 'tickdir', 'out');
% if sp == 1, title(sprintf('P%02d-S%d_rec%d', sj, session, rec), 'interpreter', 'none'); end
% end
% suplabel('Pupil signal (z)', 'y');
% print(gcf, '-dpdf', ...
% sprintf('%s/P%02d-S%d_rec%d_finalpupil.pdf', subjectdata.figsdir, ...
% sj, session, rec));
% end
% ==================================================================
% EPOCH INTO TRIALS
% ==================================================================
% load(sprintf('%s/P%02d-S%d_rec%d_contdata.mat', ...
% subjectdata.preprocdir, sj, session, rec));
assert(data.fsample == newfs, 'sampling rate error');
cfg = [];
cfg.trl = trialdefinition;
data = ft_redefinetrial(cfg, data);
% ==================================================================
% SAVE FILE
% ==================================================================
data = rmfield(data, 'cfg'); % keep the data file as small as possible
savefast(sprintf('%s/P%02d-S%d_rec%d_data.mat', ...
subjectdata.preprocdir, sj, session, rec), 'data', 'trialdefinition');
fprintf('\n\n SAVED %s/P%02d-S%d_rec%d_data.mat \n\n', ...
subjectdata.preprocdir, sj, session, rec);
end % recordings
end % session
end