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marcobarilarimarcobarilari
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add old main script to be refactored
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‎ALocalizer.m‎

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%function mirror_runMTLocalizer
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clear all;
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clc
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%8 trials = 370 sec (without trigger) =6.17 minutes
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% if TR =2 Sec. 370 sec / 2 (TR) = 185 TRs (without trigger) + 4 = 189 TRs
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% if TR =2.5 Sec. 370 sec / 2 (TR) = 148 TRs (without trigger) + 4 = 152 TRs
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%% To correct for the y-axis problem inside the scanner
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% where the lower 1/3 of the screen is not appearing because of coil indicate which device the script is running on, on PC, the middle of the
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% y axis will be the middle of the screen, on the Scanner, the middle of y-axis will be the middle of the upper 2/3 of the screen, because the
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% lower 1/3 is not visible due to the coil in the scanner.
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device = 'Scanner';
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%device = 'PC';
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fprintf('Connected Device is %s \n\n',device);
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% Original Script Written by Sam Weiller to localize MT+/V5
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% Adapted by M.Rezk to localize MT/MST (Huk,2002)
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%% Start me up
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% Get the subject Name
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SubjName = input('Subject Name: ','s');
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if isempty(SubjName)
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SubjName = 'trial';
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end
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fprintf('Auditory MT Localizer \n\n')
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%% Experiment Parametes
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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initial_wait = 5; % seconds to have a blank screen at the beginning, the scans will be discarded until % the magnetic field is homogenous
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finalWait = 5;
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%blockDur = 16; % Block duration [should be a multiple of osc (below)]
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ISI = 0.1; % Interstimulus Interval between events in the block.
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ibi = 6; % Inter-block duration in seconds (time between blocks)
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nrBlocks = 14; % Number of trials , where 1 block = 1 block of all conditions (static and motion)
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numEventsPerBlock = 12;
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range_targets = [0 2]; % range of number of targets in each block (from 2 to 5 targets in each block)
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mirror_width= 11.5; % Width (x-axis) of the mirror (in cm)
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v_dist = 14; % viewing distance from the mirror (cm) "in this script we use mirror"
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fix_r = 0.15; % radius of fixation point (deg)
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%Audiofile_duration = 16 ; % Length of the Audio file (in seconds)
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%Stop_audiofile = blockDur ; % Let the audio file play for x Seconds
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % 1 Cycle = one inward and outward motion together
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%% Experimental Design
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% function "experimental_design" while assign the blocks, conditions, and
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% the number of targets that will be used in the motion localizer
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%[names,targets,condition] = experimental_design(nrBlocks,range_targets);
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[names,targets,condition,directions,isTarget] = experimental_design(nrBlocks,numEventsPerBlock,range_targets) ;
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numBlocks = length(names); % Create a variable with the number of blocks in the whole experiment
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%% InitializePsychAudio;
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InitializePsychSound(1);
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[soundData, freq] = loadAudioFiles(SubjName);
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phandle = PsychPortAudio('Open',[],[],1,freq,2);
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%PsychPortAudio('FillBuffer',phandle,soundData_static);
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%fprintf('\nstatic wav file loaded. \n')
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%% PTB Setup
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screenNumber = max(Screen('Screens'));
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%screenNumber = 0;
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%Screen('Preference', 'SkipSyncTests', 2);
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[w, winRect, xMid, yMid] = startPTB(screenNumber, 1, [128 128 128]);
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HideCursor;
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%% Color indeces, and Screen parameters and inter-flip interval.
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% Color indices
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white = WhiteIndex(screenNumber);
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black = BlackIndex(screenNumber);
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grey = ceil((white+black)/2);
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% Flip interval and screen size
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ifi = Screen('GetFlipInterval', w); % Get the flip interval
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[tw, th] = Screen('WindowSize', w);
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%nframes = floor(blockDur/ifi);
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% while mod(nframes,2)~=0 % make sure the nframes are even number
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% nframes = nframes-1; % to be able to re-assign dots in the static condition (to perform divison calculation)
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% end
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%% Welcome screen
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Screen('TextFont',w, 'Courier New');
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Screen('TextSize',w, 20);
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Screen('TextStyle', w, 1);
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DrawFormattedText(w,'Press for FASTER sound \n\n\n(static or motion)',...
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'center', 'center', black);
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Screen('Flip', w);
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[~, ~, ~]=KbCheck;
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KbWait;
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Screen('Flip', w);
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WaitSecs(0.25);
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% DrawFormattedText(w,'The experiment is about to begin','center', 'center', black);
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% Screen('Flip', w);
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% [KeyIsDown, pend, KeyCode]=KbCheck;
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%
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% KbWait;
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% Screen('Flip', w);
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%% FUNCTION
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if strcmp(device,'PC')
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DrawFormattedText(w,'Waiting For Trigger',...
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'center', 'center', black);
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Screen('Flip', w);
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% press key
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KbWait();
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KeyIsDown=1;
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while KeyIsDown>0
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[KeyIsDown, ~, ~]=KbCheck;
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end
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% open Serial Port "SerPor" - COM1 (BAUD RATE: 11520)
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elseif strcmp(device,'Scanner')
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DrawFormattedText(w,'Waiting For Trigger','center', 'center', black);
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Screen('Flip', w);
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SerPor = MT_portAndTrigger;
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Screen('Flip', w);
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end
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%% Experiment Start (Main Loop)
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experimentStartTime = GetSecs;
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%% To correct for the y-axis problem inside the scanner
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if strcmp(device,'Scanner')
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adjusted_yAxis = 2/3*th; % where the lower 1/3 of the screen is not appearing because of coil
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elseif strcmp(device,'PC')
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adjusted_yAxis = th; % y-axis is the same, no changes
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end
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%% Pixels per degree
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[mirrorPixelPerDegree] = mirror2Pixels (winRect,v_dist,mirror_width) ; % Calculate pixel per degree on the mirror surface
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%% fixation coordiates
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fix_cord = [[tw/2 adjusted_yAxis/2]-fix_r*mirrorPixelPerDegree [tw/2 adjusted_yAxis/2]+fix_r*mirrorPixelPerDegree];
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%% Experiment start
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% The experment will wait (initial_wait) Secs before running the stimuli
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Screen('FillOval', w, uint8(white), fix_cord); % draw fixation dot (flip erases it)
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blank_onset=Screen('Flip', w);
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WaitSecs('UntilTime', blank_onset + initial_wait);
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targetTime = [];
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responseKey = [];
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responseTime = [];
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eventOnsets=zeros(numBlocks,numEventsPerBlock);
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eventEnds=zeros(numBlocks,numEventsPerBlock);
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eventDurations=zeros(numBlocks,numEventsPerBlock);
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responsesPerBlock=zeros(numBlocks,1);
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playTime = zeros(numBlocks,1);
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for blocks = 1:numBlocks
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timeLogger.block(blocks).startTime = GetSecs - experimentStartTime; % Get the start time of the block
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timeLogger.block(blocks).condition = condition(blocks); % Get the condition of the block (motion or static)
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timeLogger.block(blocks).names = names(blocks); % Get the name of the block
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responseCount=0;
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for iEvent = 1: numEventsPerBlock
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Sound=[];
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if isTarget(blocks,iEvent)==0
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if strcmp(directions(blocks,iEvent),'S')
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Sound= soundData.S;
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elseif strcmp(directions(blocks,iEvent),'U')
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Sound= soundData.U;
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elseif strcmp(directions(blocks,iEvent),'D')
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Sound= soundData.D;
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elseif strcmp(directions(blocks,iEvent),'R')
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Sound= soundData.R;
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elseif strcmp(directions(blocks,iEvent),'L')
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Sound= soundData.L;
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end
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elseif isTarget(blocks,iEvent)==1
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if strcmp(directions(blocks,iEvent),'S')
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Sound= soundData.S_T;
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elseif strcmp(directions(blocks,iEvent),'U')
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Sound= soundData.U_T;
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elseif strcmp(directions(blocks,iEvent),'D')
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Sound= soundData.D_T;
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elseif strcmp(directions(blocks,iEvent),'R')
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Sound= soundData.R_T;
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elseif strcmp(directions(blocks,iEvent),'L')
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Sound= soundData.L_T;
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end
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end
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eventOnsets(blocks,iEvent)=GetSecs-experimentStartTime;
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PsychPortAudio('FillBuffer',phandle,Sound);
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playTime(blocks,1) = PsychPortAudio('Start',phandle);
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%length(playedAudio)/freq
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while GetSecs() <= eventOnsets(blocks,iEvent)+ experimentStartTime + (length(Sound)/freq)
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if strcmp(device,'Scanner')
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[sbutton,secs] = TakeSerialButton(SerPor);
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%[sbutton,secs] = MT_TakeSerialButtonPerFrame(SerPor);
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%responseKey(end+1)= sbutton;
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if sbutton~= 0
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responseTime(end+1)= secs - experimentStartTime;
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%%%%%%%%%%%%%%%%%%%%%
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% while you are pressing, wait till it is
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% released
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while sbutton ~= 0
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[sbutton,secs]= TakeSerialButton(Cfg.SerPor);
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end
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%%%%%%%%%%%%%%%%%%%%%
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responseCount = responseCount + 1;
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end
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elseif strcmp(device,'PC')
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[keyIsDown, secs, ~ ] = KbCheck();
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if keyIsDown
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responseTime(end+1)= secs - experimentStartTime;
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while keyIsDown ==1
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[keyIsDown , ~] = KbCheck();
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end
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responseCount = responseCount + 1;
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end
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end
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end
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eventEnds(blocks,iEvent)=GetSecs-experimentStartTime;
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eventDurations(blocks,iEvent)=eventEnds(blocks,iEvent)-eventOnsets(blocks,iEvent);
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WaitSecs(ISI);
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end
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responsesPerBlock (blocks,1) = responseCount ;
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%% Get Block end and duration
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timeLogger.block(blocks).endTime = GetSecs - experimentStartTime; % Get the time for the block end
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timeLogger.block(blocks).length = timeLogger.block(blocks).endTime - timeLogger.block(blocks).startTime; %Get the block duration
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%% Fixation cross and inter-block interval
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Screen('FillOval', w, uint8(white), fix_cord); % draw fixation dot (flip erases it)
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blank_onset=Screen('Flip', w);
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WaitSecs('UntilTime', blank_onset + ibi); % wait for the inter-block interval
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end;
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% At the end of the blocks wait ... secs before ending the experiment.
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Screen('FillOval', w, uint8(white), fix_cord); % draw fixation dot (flip erases it)
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blank_onset=Screen('Flip', w);
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WaitSecs('UntilTime', blank_onset + finalWait);
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%% Save the results ('names','onsets','ends','duration') of each block
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names = cell(length(timeLogger.block),1);
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onsets = zeros(length(timeLogger.block),1);
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ends = zeros(length(timeLogger.block),1);
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durations = zeros(length(timeLogger.block),1);
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for i=1:length(timeLogger.block)
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names(i,1) = timeLogger.block(i).names;
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onsets(i,1) = timeLogger.block(i).startTime;
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ends(i,1) = timeLogger.block(i).endTime;
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durations(i,1) = timeLogger.block(i).length;
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end
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%% KeyPresses and Times
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% for i=length(responseKey):-1:2 % responseKey gives a '1' in all frames where button was pressed, so one motor response = gives multiple consequitive '1' frames
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% if responseKey(i-1)~=0 % therefore, we need to cancel consequitive '1' frames after the first button press
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% responseKey(i)=0; % we loop through the responses and remove '1's that are not preceeded by a zero
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% responseTime(i)=0; % this way, we remove the additional 1s for the same button response
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% end % - The same concept for the responseTime
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% end
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%
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% for i=length(targetTime):-1:2 % The same concept as responseKey adn responseTime.
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% if targetTime(i-1)~=0 % Our Targets lasts 3 frames, to remove the TargetTime for the 2nd and 3rd frame
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% targetTime(i)=0; % we remove targets that are preceeded by a non-zero value
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% end % that way, we have the time of the first frame only of the target
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% end
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%
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% responseKey = responseKey(responseKey > 0); % Remove zero elements from responseKey, responseTime, & targetTime
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% responseTime = responseTime(responseTime > 0);
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% targetTime = targetTime(targetTime > 0);
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%% Shutdown Procedures
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ShowCursor;
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clear screen;
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myTotalSecs=GetSecs;
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Experiment_duration = myTotalSecs - experimentStartTime;
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%% Save a mat Log file
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% Onsets & durations are saved in seconds.
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save(['logFileFull_',SubjName,'.mat']);
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save(['logFile_',SubjName,'.mat'], 'names','onsets','durations','ends','targets','responseTime','responseKey','targetTime','Experiment_duration','playTime');
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%% FUNCTION
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% close Serial Port ---- VERY IMPORTANT NOT FORGET
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if strcmp(device,'Scanner')
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CloseSerialPort(SerPor);
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end
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catch
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clear Screen;
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fprintf('Code was catched!')
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%% Close serial port of the scanner IF CRASH OF THE CODE
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if strcmp(Cfg.device,'Scanner')
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CloseSerialPort(Cfg.SerPor);
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end
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end

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