NB - as of early 2015, the method of using scanner sync in matlab has changed. The new method uses Tibor's ScannerSynchClass rather than Rhodri's MRISync / ScannerSync software, = Using ScannerSync from Matlab - NEW METHOD = = Using ScannerSync from Matlab - OLD METHOD = Make sure you have the ScannerSync control installed. Somewhere near the top of your code, set up ScannerSync & initialise communication with the input-output board (will not work if you're using a machine without the board, e.g., not the mimic or stim delivery machines). {{{ %% SCANNERSYNC TR=1000; % TR in ms numdummies=8; % Create & initialise scanner sync object objSS=actxserver('MRISync.ScannerSync'); %Create a scanner object invoke(objSS,'Initialize','') %Initialise the Keithley board and object invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling }}} Now, wait for first pulse from scanner. Also, tell ScannerSync the approximate TR. {{{ % ScannerSync - waits for the first pulse, resets timer to 0, sets TR invoke(objSS,'StartExperiment', double(TR)); }}} Wait for dummies (one less as StartExperiment command above will already have heard a pulse) {{{ for countdown=(numdummies-1):-1:1 count_text=sprintf('%d', countdown); % uncomment the next two if you're using the PsychToolbox % DrawFormattedText(window, count_text, 'center', 'center', white); % Screen(window, 'Flip'); invoke(objSS,'SynchroniseExperiment',1,0); % 1= force wait for actual pulse; 0=return this many ms after pulse end; }}} In your trial loop, you'll need to spend some of the time listening for pulses {{{ invoke(objSS,'CheckPulseSynchronyForTime', double(500)); % spend 500 ms listening for any pulses }}} You should dump out the timing of critical events and the measured TR {{{ picstarttime=invoke(objSS,'SSGetTimer'); measuredTR=invoke(objSS,'GetMeasuredTR'); % ...add your own code to write these to your output file }}} Also, for some designs you may want to occasionally synchronise your trials to the scanner {{{ invoke(objSS,'SynchroniseExperiment',1,0); % 1= force wait for actual pulse; 0=return this many ms after pulse }}} == Using pretend mode == If you'd like to test code on a machine without the card, you may use a feature of ScannerSync called "pretend mode". To do this: (1) When in pretend mode, don't do "Initialise", and instead issue a "SetPretendMode" command. So change the first block to something like {{{ pretendmode=1; % Create & initialise scanner sync object objSS=actxserver('MRISync.ScannerSync'); %Create a scanner object if (~pretendmode) invoke(objSS,'Initialize','') %Initialise the Keithley board and object else invoke(objSS,'SetPretendMode',1) end; invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling }}} (2) You'll then see a warning message when you get to the "StartExperiment" command, to which you should click "OK". If you're using the PsychToolbox and have already set up the screen, make sure that you only use the HideCursor command after the StartExperiment command, otherwise you won't be able to click OK. If you would like to use the button box in the practice room of the Scanner building, you will need this code instead to make the button box work: {{{ pretendmode=1; % Create & initialise scanner sync object objSS=actxserver('MRISync.ScannerSync'); %Create a scanner object if (~pretendmode) invoke(objSS,'Initialize','') %Initialise the Keithley board and object else invoke(objSS,'SetPretendModeExtended',1,0) invoke(objSS,'Initialize','') %Initialise the Keithley board and object end; invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling }}} == Collecting Responses == To collect responses in matlab using the button box add a code similar to this: {{{ tic resp=0; gotresp=false; while toc