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= Using ScannerSync from Matlab = | ***** |
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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 = Open Matlab and check that the ScannerSynchClass is on the path, e.g. using: which ScannerSynchClass Create an instance of the ScannerSynchClass SSO= = Using ScannerSync from Matlab - OLD METHOD = |
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numdummies=8; | numdummies=8; |
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invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling | invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling |
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Wait for dummies (one less as StartExperiment command above will already have heard a pulse) | |
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Wait for dummies (one less as StartExperiment command above will already have heard a pulse) | |
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end; | end; |
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In your trial loop, you'll need to spend some of the time listening for pulses | |
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In your trial loop, you'll need to spend some of the time listening for pulses | |
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You should dump out the timing of critical events and the measured TR | |
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You should dump out the timing of critical events and the measured TR | |
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}}} Also, for some designs you may want to occasionally synchronise your trials to the scanner |
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}}} Also, for some designs you may want to occasionally synchronise your trials to the scanner |
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invoke(objSS,'SetPretendMode',1) | invoke(objSS,'SetPretendMode',1) |
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invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling | invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling |
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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: | 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: |
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invoke(objSS,'SetPretendModeExtended',1,0) invoke(objSS,'Initialize','') %Initialise the Keithley board and object |
invoke(objSS,'SetPretendModeExtended',1,0) invoke(objSS,'Initialize','') %Initialise the Keithley board and object |
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invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling | invoke(objSS,'SetMSPerSample',2); %Set StartExperiment routines’ sampling |
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This will collect the responses made by the subject during a pre-defined time interval (rt_window). You can also need to define which buttons the subject should press (in this example they are called samekey and diffkey). The codes returned by pressing the buttons are 28, 26, 22, 14 (i.e. when the right hand is placed on the button box and the subject used his index finger the code returned will be 28). | |
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This will collect the responses made by the subject during a pre-defined time interval (rt_window). You can also need to define which buttons the subject should press (in this example they are called samekey and diffkey). The codes returned by pressing the buttons are 28, 26, 22, 14 (i.e. when the right hand is placed on the button box and the subject used his index finger the code returned will be 28). | The GetResponse() function will by default only return first four button presses. If there is a need to use more than 4 buttons one could use GetResponseExtended() or ReadPIOValue(). The example below uses the latter function and ignores responses 254 and 255, which relate to no-response events. |
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== Collecting Responses Times == |
{{{ tic resp=0; gotresp=false; while toc<rt_window if (~gotresp) resp=invoke(objSS,'ReadPIOValue'); if isempty(intersect([255,254],resp)) gotresp=true; end; end; end; }}} == Collecting Response Times == |
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rt=invoke(objSS,'SSGetTimer')-respstarttime; %or alternatively you can set rt=toc | rt=invoke(objSS,'SSGetTimer')-respstarttime; %or alternatively you can set rt=toc |
*****
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
Open Matlab and check that the ScannerSynchClass is on the path, e.g. using:
which ScannerSynchClass
Create an instance of the ScannerSynchClass
SSO=
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<rt_window if (~gotresp) resp=bitand(30,invoke(objSS,'GetResponse')); if (resp==samekey || resp==diffkey) gotresp=true; end; end; end;
This will collect the responses made by the subject during a pre-defined time interval (rt_window). You can also need to define which buttons the subject should press (in this example they are called samekey and diffkey). The codes returned by pressing the buttons are 28, 26, 22, 14 (i.e. when the right hand is placed on the button box and the subject used his index finger the code returned will be 28).
The GetResponse() function will by default only return first four button presses. If there is a need to use more than 4 buttons one could use GetResponseExtended() or ReadPIOValue(). The example below uses the latter function and ignores responses 254 and 255, which relate to no-response events.
tic resp=0; gotresp=false; while toc<rt_window if (~gotresp) resp=invoke(objSS,'ReadPIOValue'); if isempty(intersect([255,254],resp)) gotresp=true; end; end; end;
Collecting Response Times
To collect RTs you could try the following:
resp=0; gotresp=false; respstarttime=invoke(objSS,'SSGetTimer'); tic while toc<rt_window if (~gotresp) resp=bitand(30,invoke(objSS,'GetResponse')); if (resp==samekey || resp==diffkey) rt=invoke(objSS,'SSGetTimer')-respstarttime; %or alternatively you can set rt=toc gotresp=true; end; end; end;