SpinozaWiki:General stimulus setup

MRI scanner

Philips Achieva XT 3T 32 channel recieve headcoil. Dual pulse RF excitation. Width of MRI-tube: 58 cm.

Visual Stimulus Presentation

Maximum resolution of beamer: 1920x1200 (ATI Radeon HD 7750 with 4Gb onboard memory).
Stimulus computer resolution: 1920 x 1200 pixels (60 Hertz refresh rate, always one frame delay (as every DLP beamer)).

Projection screen: width x height: 61 cm x 36 cm (size of projected image). Mirror: width x height: 17 cm x 10 cm.
Distance mirror - eye: 8 cm.
Distance projection screen - mirror: 113 cm
Distance projection screen - start of of bed: 73 cm
Distance start of of bed - mirror: 40cm
Distance beamer - projection screen: 210 cm.

Calculating the Visual Angle

The visual angle is a way to measure the size of an object on a monitor or project screen as it appears to the subject.
This is relative to the size of the projection and the distance between the subject and the screen.

Here and example of how to calculate the visual angle of a certain stimulus presented on a screen.

The example below shows computation of the visual angle subtended when the extent of the stimulus and viewing distance are different, as is the case when you do a behavioural study using a computer monitor and afterwards doing an MRI study.

When you do a fMRI study and you want to transform your stimuli to keep them at the same visual angle you need the following measures:

Projection on screen: 125*93,7 cm (not everything on screen)
mirror to screen: 331 cm
eye to mirror: ±10 cm

If you want to know what the size of your stimuli will be on the projection screen at the AMC that the ratio between your screen length and that of the size of the projection at the AMC and use this to calculate the new size of your stimuli (and after that you can calculate the new visual angle).

Example: screen width K14/K15 = 41 cm screen width AMC standard = 108 cm. Ratio => 1: 108/41 = 1: 2,6341

   1: 81/30,7= 1: 2,6341 

If size on screen k14/k15 = 1cm than it will be 1x 2,6341= 2,6341 cm!! on the projection screen. (aha!)

Subject responses [Presentation and EPrime]

button boxes
these only use one forp 932 interface.

Button codes are:
right hand responses enter the system as:
right index finger : b
right middle finger: y
right ring finger  : g
right pinky finger : r

Left hand responses enter the system as:
left index finger : e
left middle finger: w
left ring finger  : n
left pinky finger : d

the following settings are for the 2x4 response buttons

Make sure the settings on the forp 932 interface match the picture below 

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2x4 button box (HHSC-2x4-C)

On the forp 932 you should set the correct values for this 8 button device. The model number of the 8 Button Bimanual Curved Lines is “HHSC-2x4-C”. Furthermore we need to set the correct mode of operation. We prefer the letter output (BYGREWND) including a “t” for each trigger sent by the MRI scanner (Mode 002 with HID NAR BYRGT). Mode 000 with HID KEY BYRGT works as well, but for compatibility issues with the Matlab Psychtoolbox we prefer the NAR mode by default. Only the response buttons give the possibility to send a trigger on each scanner TR (as a simulated keyboard "t" output), with a trackball or a joystick the simulated keyboard “t” output is not available.

Change the forp operation mode or button box connected:

AUTOCONFIGURE
After the buttons boxes are changed (even if the new button box is of the same type) use AUTOCONFIGURE (or Manual config) and re-select the operating mode (in order to make the device adjust the gain properly on all channels (sort of calibration)).
Instructions:

- Push the knob on the forp 932 interface.(turn knob to change selection and press knob to execute)

- Change modes -> Yes

- AUTOCONFIGURE

- Correct button box model should be already set (default HHSC-2x4-C)

- we use the USB interface

- Select correct mode (default Mode 002 with HID NAR)

if the AUTOCONFIGURE option doesn't work you may want to try the MANUAL configuration (see below). Please inform the tech support about the problem.
More information about different operation modes: http://www.curdes.com/technical/932usemodes The getting started guide: http://www.curdes.com/technical/932-Getting-Started

Manual config

- Push the knob on the forp 932 interface.

- Change modes -> Yes (turn knob to change selection and press knob to execute)

- Manual config

- we use the USB interface

- Select correct model ("HHSC-CYL-5" (= 5 button cylinder) or “HHSC-2x4-C” (=2x4 button box))

- Select correct mode (default Mode 002 with HID NAR)

Joystick settings
We have the possibility to use a MR compatible joystick as well. At this time we have the joystick connected to the second forp response box controller. So under normal circumstances there is no need to make any adjustments. If you want to use the joystick in you experiment you need to program your script as if you use a regular two button mouse.

the following settings are for the joystick:

Please note: the keyboard "t" trigger isn't available when you select the joystick mode. So you need to use the LPT trigger method as described on #Triggering of stimulus software (complex & no jitter) wiki page.

Make sure the settings on the forp 932 interface match the picture below

To change the settings:

- Push the knob on the forp 932 interface.

- Change modes -> Yes (turn knob to change selection and press knob to execute)

- AUTOCONFIGURE

- Correct button box model should be already set (HHSC-joy-1)

- we use the USB interface

- Select correct mode (default Mode 600 -> joystick mouse)

E-prime2 and PsychToolbox

The default stimulus program is Presentation. Hereby some extra information for programs like E-Prime2 and PsychToolbox (not supported by the Technical Support Psychology (aka TOP))

Responses in PsychToolbox:
Make sure the USB-converter (fORP 932) device is in a mode that generates keycodes with NAR (non auto-release). This causes keyboard-like behavior with pulses that continue for the duration of the press. Matlab is now able to register the first pulse(s) from that press, just as with a keyboard. Since Presentation can handle both modes we made the NAR option the default. However if you experience response button issues make sure to check if the fORP 932 response controller has indeed the NAR option enabled.

more information: http://www.curdes.com/technical/matlab_ptb

E-Prime2 & PsychToolbox(?) port codes
output port
Some stimulus software requires you to specify the address of the port you want to use (for Presentation a reference to LPT1 suffices). However the parallel port (= printer port = LPT1) is not at the default address.
To sent a trigger out you normally would use something like:
WritePort &H378, 1
However the port addresses used in the MRI scanner computer differ. These are "C040" and "C050". I assume the "C050" holds the output port range (not tested) and "C040" hold the input range (again not tested).

So the E-Prime2 code would be something like:
WritePort &HC050, 1

input port
If you use the input port in E-Prime you also need to specify the port address. Here I'd expect you need to use the &HC040 address:

Triggering of stimulus software (simple & 2 ms jitter)

With each BOLD-MRI volume a trigger is sent to the stimulus computer. These enter the system as:

the letter t
(as in a keyboard response)

The way to set this up in Presentation is illustrated below:

Select Use response button event.

Select Use fMRI (on the right side of buttons) after you selected the letter t.

If the setup went correctly you should see 'Keyboard: T' beneath Use response button event.

Triggering of stimulus software (complex & no jitter)

The above describe procedure (simple) works perfectly well if you are prepared for a 4 ms jitter between actual scan pulse and registered scan pulse. If this is not acceptable you will need to use the parallel port for reading in the trigger.

The correct settings (in Presentation) for the parallel port are displayed below:

The correct settings for the parallel port settings are displayed below:

You may need to make some simple hardware adjustments as well. On the shelf on top of the stimulus computer you’ll find a “TR trigger switch”. The two switches on this box need to be in the right position in order to work. Explanation of the picture below:

A -> NI connector -> Green LED to indicate this connector is active (this is an old option and should not be used anymore).

B -> parallel port connector -> Green LED to indicate this connector is active

C -> switch to control the port device used (either NI-6503 or parallel port)

D -> option switch to switch between MRI trigger mode or a response(“mri trg” is default value)

For normal operation we only use switch "C" to select the port device we want to use.

MRConfon sound system

The MRConfon sound system obtains its power from the magnetic field. This allows the system to produce a surprisingly powerful sound signal. This also means it is crucial to check your sound levels with the headphones entirely inside the scanner. Outside the bore the headphones produce almost no sound, inside the bore the sound-level is much higher.

Use "master volume" knob to adjust the main volume (8.75 by default). This is the only knob you're allowed to use on the audio amplifier.
Default settings:

- In the left LCD "FMRI-BAL" should read "CENTER". Only use the "BALANCE left vol" knob only to restore the default settings.

- On the right LCD the "SRC:" (source obviously) should read "IN STIM". Press the "start" button only to restore the default settings.

monitor speakers

- we've put a cord switch on each speaker wire to make it possible to completely mute the monitor sound.

- It's possible to alter the volume of the monitor speakers as well. Just press the big volume knob (S-Mon-Vol appears in left LCD display) and adjust the volume.

troubleshooting
If you experience any difficulties (no sound for subject, operator mic not working, etc.) it is highly recommended to restart the amplifier. The on/off button is on the rear left side (push button similar to those in the front panel).

EEG EGI system (256 channel)

The scanner is equipped with a 256 channel EGI system (http://www.egi.com/research-division-research-products/research-division-research-products-mr-compatible).

Important note: port code "1" is reserved for the electric stimulator,
so for now only use port codes that don't include the first bit. 
2, 4, 8, 16, 32, 64, 128 represent the separate output pins and all even numbers from 2 till 254 will work.

EGI GSR

Note that this is just a short description of how to use the GSR. If you want to use it for your experiment please contact Tinka Beemsterboer

We’ve invested considerable time and effort in writing an EGI GSR manual. You can download the manual here. Please follow the instructions in the manual carefully.
File:EGI GSR v1.2.pdf

Although the short custom manual provides the necessary information to quick start the EGI-GSR setup it is highly recommended to study the EGI NetStation manual as well. The “NetStation_Acquisition” manual explains all about the setup of NetStation in order to acquire your physiological data. The NetStation “Waveform Tools” manual explains the further details about data analysis. Here probably the filter and export options of the NetStation software is most interesting. Don’t forget to apply the data correction patch before you alter your data in any way.
File:NetStation Acquisition.pdf
File:Waveform Tools.pdf

When we measure physiological data like GSR and EMG we use the PIB input box. Therefore it’s good to know the PIB channels are treated somewhat different in NetStation. The filtering of the PIB channels is configured in a separate file. So if you want to alter the filter settings for the PIB channels you need to change this file or make a new PIB filter settings file. The “PIB_Text_File_Alteration” manual below explains in detail how to do this.
File:PIB Text File Alteration.pdf

Please note you need to apply a correction to the NetStation output file. Please note this should be the first step after recording your experiment and you can only correct the original NetStation output file. You can’t correct data that is already filtered or MRI artefact corrected.
You can download the program to correct the GSR output at the following link:
http://labs.psychologie.uva.nl/binaries/content/assets/subsites/technische-ondersteuning-psychologie/downloads/convertgsr.zip

Important note: port code "1" is reserved for the electric stimulator,
so for now only use port codes that don't include the first bit. 
2, 4, 8, 16, 32, 64, 128 represent the separate output pins and all even numbers from 2 till 254 will work.

The instructions of how to use this program are included in the EGI GSR manual. Or you can use these instuctions:

File:How to ConvertGSR 1.pdf

Eyetracking

An Eyelink 1000 eyetracker, with fiber optic camera upgrade (SR Research) is permanently mounted alongside the stimulus display. The eyelink is powered by MRI compatible batteries.

SR research provides an excellent EyeLink 1000 user manual. If you use this system it is highly recommended to read the manual. It explains all options in detail and provides some nice recommendations to optimize the EyeLink output.

For the EyeLink manual follow this link:
File:EyeLink1000 UserManual.pdf

Conditioning

Note that this is just a short description about using the electrical stimulator.
Ones you've decided use the electrical stimulator during your experiment, it is your own responsibility to read literature about settings, where to place the electrodes and how to handle your participant in a mr-conditioning experiment. Furthermore you need to follow a course to become certified to use the equipment. Please contact Tinka Beemsterboer for more information.

The standard settings are:
2000 microseconds
400 Volt
x10 mA
Output switch up
start with 0.00

To trigger the electrical stimulator you need to configure your stimulus software to 
send code "1" to the output port (=printer port/parallel port/LPT1).

Place the MR compatible carbon electrode stickers (Kendall H135TSG) on the leg or wrist (something you have to decide for yourself). Use the carbon pinch lead to connect the disposable electrodes, you can find these in the storage unit in the operator room. It is absolutely prohibited to use other electrodes / leads because this may compromise subject safety. Tell your participant you increase the pulse strength up to a level that it is really inconvenient but not painful. Determine the pulse strength before starting the scans. Make sure your participant hears you and that you can hear him/her by keeping the MR door open.

If you deviated from the standard settings make sure to use the checklist NeuroWiki:Checklist after scanning

medigoggles

Click here to find the user instructions.