1. ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Matlab: Cogent & External Devices Friederike Schüür 18th March 2010 Course Material: http://www.icn.ucl.ac.uk/http://www.icn.ucl.ac.uk/ Cogent Software: http://www.vislab.ucl.ac.uk/cogent.phpuk/cogent.php

2. ICN Matlab for Cognitive Neuroscience 2009 /10 – Presenting Stimuli with Cogent Initialising expt. variables start_cogent Run experiment - load premade stimulus files - create new stimuli - trial loop: - present stimuli - get user responses - save data as you go - save final data & close files stop_cogent Configuration of devices Basic script overview: recap In the previous sessions we covered: General structure of cogent scrips Presentation of stimuli Visual Sound Registration of keyboard & mouse events Logging & saving of data Communication with external devices!

3. ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Todays lecture: Ext. devices Using a button box Synchronization with external devices MRI scanner Check sound or display synchronization Sending triggers to: TMS EEG serial port... parallel port... Configuration of devices + some cogent commands General Usage:

4. 4 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Whats a serial port? A serial port is a serial communication interface. Information transfers in or out one bit at a time. Largely obsolete in modern computers (too bad for us...). Diagrammatic oscilloscope trace of voltage levels for an uppercase ASCII K character with 1 start bit, 8 data bits, and one stop bit (RS-232).

5. 5 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Configuration of the serial port Configuration : config_serial(port, baudrate, parity, stopbits, bytesize) port: - COM port number (1,2,3,4, etc.) baudrate: - (110, 300, 600,..., 128000, 256000) parity: - (0 = none, 1 = odd, 2 = even, 3 = mark, 4 = space) stopbits: - (0 = 1, 1 = 1.5, 2 = 2) bytesize: - (4 bits, 8 bits) Default setting: config_serial(1, 9600, 0, 0, 8) which is used if config_serial is used without input arguments.

6. 6 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Jargon of the serial port config_serial(port, baudrate, parity, stopbits, bytesize) port: Number of the serial port youre going to use. baudrate: Number of symbols transmitted per second (similar to bit rate). parity: Simple form of error detection in data transmission. E.g. if you choose even parity, then parity bit set to 1 is nr. of 1s is odd in data transmission making number of transmitted 1s even. If nr. of transmitted 1s then odd: error! (mark parity = bit always 1, space parity = bit always 0). stopbits: Allow receiving signal hardware to detect the end of a character. bytesize: Number of bits per byte. Default setting: config_serial(1, 9600, 0, 0, 8) which is used if config_serial is used without input arguments.

7. ICN Matlab for Cognitive Neuroscience 09 /10: Recording, logging & saving with Cogent readserialbytes(port) ----------------------------------------------------------------------- reads all bytes arriving at serial port 1 & empties the buffer (clearserialbytes(port)) logserialbytes(port) ----------------------------------------------------------------------- logs & time stamps all serial bytes that have been read by last readserialbytes. Saved in a logfile if configuered. clearserialbytes(port) ----------------------------------------------------------------------- empties the buffer for serial port number Serial port: button box

8. ICN Matlab for Cognitive Neuroscience 09 /10: Recording, logging & saving with Cogent waitserialbyte(port, time, b) ----------------------------------------------------------------------- waits a time (time in ms) for a serial byte with value b to arrive at serial port number port. Executes readserialbytes and logserialbytes. All serial bytes are logged, and the buffer is emptied. If time time elapsed before b has arrived, then the script continues. Serial port: button box [k t n] = getserialbyte(port) ----------------------------------------------------------------------- returns values and times of serial bytes read by readserialbytes

9. 9 ICN Matlab for Cognitive Neuroscience 09 /10: Recording, logging & saving with Cogent %Correct %defining variables trial_no = 10; trial_dur = 15000; clearserialbytes(1); %empty buffer for p = 1:trial_no; wait(trial_dur) % allow some time to pass readserialbytes(1); [k t n] = getserialbytes(1); % update & extract bytes keys(p).k = k; keys(p).t = t; end; Example: button box Loop round 10 x 15sec trials, get button presses Depends on specific button box, usually: 0, 1, 2, 4, 6.

10. 10 ICN Matlab for Cognitive Neuroscience 09 /10: Recording, logging & saving with Cogent Incoming pulses generated by the external device can be used for synchronization. The stimulus computer waits until the signal is registered. Commands used for this operation are: clearserialbytes(1) waitserialbytes(1,inf, byte_to_wait_for). Once the byte_to_wait_for has been received, the script continues. Example: Synchronization Ensure that stimulus computer & external device are in synchrony.

11. 11 ICN Matlab for Cognitive Neuroscience 09 /10: Recording, logging & saving with Cogent Depends on serial port (getslice reads serial port) use code available at: http://www.fil.ion.ucl.ac.uk/local/mri/home/ericf/cogent2000.html [slices, times] = getslice( port ) % returns most recent slice number with time stamps. logslice %transfers scanner slices read by getslice to the log file [s, t] = waitslice( port, n ) %waits forever for MRI slice n or greater, returns actual slice number and time stamp. Example: Synchronization with the FIL MRI scanner.

12. 12 ICN Matlab for Cognitive Neuroscience 09 /10: Recording, logging & saving with Cogent Serial port can also send signals to other devices, e.g. oscilloscopes. For this, you need a special cable (see Cogent user manuals for instructions or ask Martin! ). You can generate a signal using: cgsignal (port, signal) Signal = signal code (0/1/2/3/4 etc.) or sendserialbytes (port, byte) byte needs to be between 0 – 255. Example: Sound or Display Check sound or display synchronization

13. 13 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Whats a parallel port? Interface for connecting peripherals. Transmits particular amounts of bits (e.g. 8) in parallel at the same time. Problems with accessing the parallel port: For security reasons, accessing is parallel port is blocked on most newer computers. However, you can open up the ports by e.g. using Userport which is included in the cogent download. UserPort.sys is a driver that gives access to the I/O Ports. Needs to be installed once on each computer you use.

14. 14 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Essential links For.dll files for parallel port communication: http://www.fil.ion.ucl.ac.uk/local/mri/home/ericf/cogent2000.html For problems with I/O access: http://www.beyondlogic.org/porttalk/porttalk.htm

15. 15 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Configuration of the parallel port Parallel ports usually have decimal addresses: e.g. 888, 632, or 956. Configuration: startportb(port) e.g. starportb(888) Note: startportb might not be necessary, depending on your parallel port access (the one exception for configuration... !) Controlling parallel port input: k = inportb(port) Returns decimal values of bytes arriving at port port. Controlling parallel port output: outportb(port, num). Send the number num to specified port. Num between 0 - 255.

16. 16 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Sending triggers to TMS / EEG Use outportb(port,num); wait(t_ms); outportb(port,0); to send a t_ms long pulse. If parallel port of stimulus computer (sending) is connected to an EEG setup (receiving) then num determines the pulse ID in an EEG trace. If particular bits sent by the parallel port send pulses to different external devices, e.g. to trigger data recording or a TMS machine, then num will determine which device receives the trigger. This allows triggering multiple devices from within a Matlab Cogent Script. Check carefully for delays! Problems in the past!

17. 17 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Use outportb(port,num); wait(t_ms); outportb(port,0); num is a number between 0 and 255. Its meaning is clear once its transformed into binary code. e.g. 4 corresponds to 100 send bit 2 with this command, you would send a pulse to the devices connected to bit 2 (note, count from right, the first zero corresponds to bit 0). This way you can send pulses to one or multiple devices at the same time. Sending triggers to TMS / EEG

18. 18 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Use outportb(port,num); wait(t_ms); outportb(port,0); Bit 0 to TMS machine 1 Bit 1 TMS machine 2 Bit 2 trigger DAQ computer Example: paired pulse TMS

19. 19 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices % Trigger TMS 1000ms after stimulus presentation. Start data recording after % 100ms before TMS trigger TMS.dly = 1000; TMS.intl = 2; TMS.pre_rec = 100; % Define times cgdrawsprite(1,0,0,0); % draw stimulus in buffer cgflip(0,0,0); % present stimulus t_present = time; % get time of stimulus presentation waituntil(t_present + TMS.dly - TMS.pre_rec); %wait until start recording outportb(888,4);wait(1);outportn(888,0); %start recording (4 = 100b) Example: paired pulse TMS

20. 20 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices waituntil(t_present + TMS.dly); %wait until first TMS pulse outportb(888,2);wait(1);outportn(888,0); %1st TMS pulse (2 = 10b) waituntil(t_present + TMS.dly + TMS.intvl); %wait until 2nd TMS pulse outportb(888,1);wait(1);outportn(888,0); %2nd TMS pulse ( 1 = 1b) Important: Use waituntil (not wait) otherwise timing inaccuracies. Example: paired pulse TMS

21. 21 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Not with the commands introduced … Use the Matlab Data Acquisition Toolbox. Very flexible use of parallel & serial ports and other interfaces. More advanced communication

22. 22 ICN Matlab for Cognitive Neuroscience 2009 /10 – Matlab: Cogent & External devices Next session: Sam Schwartzkopf about alternatives to Cogent for stimulus presentation: Psychophysics toolbox. Thats it for this time...