stimMakeBoldSatExperiment.m

function stimMakeBoldSatExperiment(stimParams, runNum, stimDurationSeconds, TR, movementRate, movementRateIndex)
% stimMakeTaskExperiment(stimParams,  runNum, TR)

site = stimParams.experimentSpecs.sites{1};

%For 0.33Hz, each trial consisted of three visual cues (the red circle
%turning green similar as in the first part, for 400 ms), presented at 3 s
%intercue interval, instructing the subject to close and open their hand,
%thus resulting in 0.33 Hz movement. In the second, third, and fourth
%tasks, respectively, 4, 7, or 13 cues were given with 2, 1, and 0.5 s
%intercue interval. Each trial was followed by a rest period until a total
%trial duration of 19 s was reached. Each task consisted of 13-15 trials of
%19 s.

numberOfTrialsPerRun  = 15; 
movementOnDuration    = 6;
frameRate             = stimParams.display.frameRate/2;
% NOTE Jan 16, 2019: We're specifying stimulus sequence at half the
% framerate (every other frame) because PsychToolbox presentation accuracy
% is impacted if we tell it to flip for every frame

% Determine trial length
switch lower(stimParams.modality)
    case 'fmri'        
        movementOffDuration = 15;
        preScanPeriod       = 12;
    case {'ecog' 'eeg' 'meg'}
        movementOffDuration = 6;
        preScanPeriod       = 3;
end

% Compute the length of each trial
trialDuration = movementOnDuration+movementOffDuration;

% for fMRI, we need to synchronize the onsets with the TR
switch lower(stimParams.modality)
    case 'fmri'
        preScanPeriod = round(preScanPeriod/TR)*TR;
        trialDuration = round(trialDuration/TR)*TR;
end
postScanPeriod = preScanPeriod; % seconds

% Generate trial onsets
trialOnsets = cumsum([preScanPeriod ones([1 numberOfTrialsPerRun-1])*trialDuration]);

% Derive indices into the stimulus sequence (defined at half the frameRate)
trialOnsetIndices  = round(trialOnsets*(frameRate))+1;

% Define total length of experiment
experimentLength = trialOnsets(numberOfTrialsPerRun)+trialDuration+postScanPeriod;

% Create a stimulus struct
stimulus = [];
stimulus.cmap       = stimParams.stimulus.cmap;
stimulus.srcRect    = stimParams.stimulus.srcRect;
stimulus.dstRect    = stimParams.stimulus.destRect;
stimulus.display    = stimParams.display;

% No images are shown in this experiment, just fixation dot. So we just use
% the empty placeholder images from stimInitialize
stimulus.images     = stimParams.stimulus.images(:,:,end);

% Specify stimulus sequence at frame rate resolution
stimulus.seqtiming  = 0:(1/frameRate):experimentLength;
stimulus.seq        = ones(size(stimulus.seqtiming));

% For this motor task, the fixation changes are the task instructions
% (clench vs rest). So the fixation sequence is the one that needs to be
% filled with the movement cue onsets
stimulus.fixSeq     = stimulus.seq;

% Add the repeated movement cues 

% Compute movement onsets at specified rate
movementOnsets = 0:(1/movementRate):movementOnDuration;

% Round to multiples of half the frameRate
movementOnsets  = round(movementOnsets*frameRate)/frameRate;

% Find the corresponding indices in the stimulus sequence
movementOnsetIndices  = movementOnsets*(frameRate)+1;

% Compute how many images are needed for each cue
imagesPerTrial = round((movementOnsets(end)+stimDurationSeconds)*(frameRate));
imagesPerMovement = round(stimDurationSeconds*(frameRate));

% Generate sequence of movements onsets per trial
sequencePerTrial = ones(1,imagesPerTrial);
sequencePerMovement = ones(1,imagesPerMovement)+1; % cue color change is 2
for ii = 1:length(movementOnsets)
    indices = round(movementOnsetIndices(ii)) + (0:imagesPerMovement-1);
    sequencePerTrial(indices) = sequencePerMovement;
end

% Add all trials together
for ii = 1:numberOfTrialsPerRun
    indices = trialOnsetIndices(ii) + (0:length(sequencePerTrial)-1);
    stimulus.fixSeq(indices) = sequencePerTrial;
end

stimulus.onsets = trialOnsets;

% Describe stimuli 
stimulus.cat            = [1 movementRateIndex+2]; % 3,4,5 or 6, see BAIR trigger spec
stimulus.categories     = {'REST', 'CLENCH'};
stimulus.movementRate   = movementRate; 

% Add triggers for non-fMRI modalities
switch lower(stimParams.modality)
    case 'fmri' 
        % No trigger sequence needed
    otherwise
         % Write binary trigger sequence:
        stimulus.trigSeq = zeros(size(stimulus.seqtiming));
        stimulus.trigSeq(trialOnsetIndices) = stimulus.cat(2);
        stimulus.trigSeq(1)      = 255; %experiment onset
        stimulus.trigSeq(end)    = 255; %experiment offset
end

% Sparsification is OFF for motor because we need to sample data glove at
% rate very close to stimulus frame rate 
%maxUpdateInterval = 0.25;
%stimulus = sparsifyStimulusStruct(stimulus, maxUpdateInterval);

% Create stim_file name
fname = sprintf('%s_boldsat%d_%d.mat', site, movementRateIndex, runNum);

onset       = reshape(round(stimulus.onsets,3), [length(stimulus.onsets) 1]);
duration    = ones(length(stimulus.onsets),1) * stimDurationSeconds;
trial_type  = ones(length(stimulus.onsets),1) * stimulus.cat(2);
trial_name  = repmat(stimulus.categories{2}, length(stimulus.onsets),1);
stim_file   = repmat(fname, length(stimulus.onsets),1);
stim_file_index = repmat('n/a', length(stimulus.onsets),1);
   
stimulus.tsv = table(onset, duration, trial_type, trial_name, stim_file, stim_file_index);
stimulus.site = site;

% Save
fprintf('[%s]: Saving stimuli in: %s\n', mfilename, fullfile(vistadispRootPath, 'StimFiles',  fname));
save(fullfile(vistadispRootPath, 'StimFiles',  fname), 'stimulus')

end