MR Hardware
MR Scanner
The MR Scanner is in room 065 of the CNI suite in Jordan Hall.
MR Simulator
The MR Simulator (mock scanner) is in room 062 of the CNI suite in Jordan Hall.
Stimulus Presentation
Flat Panel
The 30 inch diagonal (76 cm, 16:10 aspect ratio) flat panel display was built by Resonance Technology. This particular system is not described on their web-site (that we can see). We contacted the vendor, and they decided to modify a display for our needs. The display system is based on a Samsung LCD panel, similar (maybe identical?) to that used in the Dell Untrasharp U3011 and the HP ZR30w. At the moment, The display is positioned at the back of the bore (70cm from the top shroud around the bore, total viewing distance of 190cm). The display width is 25.5 inch (64 cm). The total field of view at this distance is about 20 deg. We believe we can safely move the display a bit closer to the bore and achieve a total width closer to 30 deg. We will be testing this shortly.
The display has a native resolution of 2560x1600, 7ms temporal response, and 10-bit color rendering. With a field of view of 30 deg (22) this produces about 80 (110) samples per deg of visual angle.
The display is driven by a dual-link DVI-to-fiber converter to pass clean digital signals into the scan room. If you do not drive the system with a dual-link capable computer, you can not achieve the native resolution. In that case, we suggest that you use 1280x800 (half-native). Note that you must drive this system with a digital signal (DVI-D, dual-link DVI-D, or HDMI via a HDMI-to-DVI-D adapter such as the one found in the CNI control room). A simple VGA-to-DVI adapter will not work, as it outputs analog DVI-A signals. Unfortunately, we have not found a VGA-to-DVI-D converter that works reliably with this system. If your laptop does not have a digital output (DVI, HDMI, or display port), then it is time to get a new laptop!
Goggles
The Resonance Technology VisuaStimDigital provides a goggle display that provides a large field of view (~40 degrees wide) and the ability to easily present different stimuli to each eye. With the goggles, you can create an immersive 3d environment or present stereoscopic visual stimuli. However, the image quality of the goggle system is not nearly as good as that of the flat panel display. The resolution is lower (800x600), the color rendering is much poorer, the gamma curves are odd, and there are some ghosting artifacts due to the analog signals.
The goggles are a tight fit in the head coils. To get them in, first position the subject with the coil slid back out of the way. Then, position the goggles in the coil and slide the coil and goggles together over the subject's face. Note that for some subjects with large heads, the goggles might not fit comfortably in the 32-channel coil.
Auditory
The auditory system is part of the Resonance Technology VisuaStimDigital. (TO DO: Add more info here.)
Olfactometer
The McClure lab will maintain a 32-channel olfactometer. (More info soon.)
Subject measurement
Response Box
We have a modular response box system (fORP 932) from Current Designs. With ths system, you can swap out various response devices. The output from any of these devices is available from the fORP box via USB. The device emulates a USB keyboard. (Note that we have found more reliable operation with PsychToolbox by using the "USB HID NAR" mode rather than the "USB HID KEY" mode. With KEY mode, some keypresses are missed.) We have confirmed that the fORP 932 USB interface is polled at 1kHz. The device itself has sub-millisecond time resolution (see the fORP FAQ). We estimate that this system provides response time measurements with a precision and reliability of about one millisecond.
The response devices that we currently have are:
- scroll-wheel device
- bimanual button boxes
- trackball device (on back-order; should arrive in a couple of weeks)
- 4-button stick-style response device.
If you have a need for a different response device, just let us know.
To use a response device at the CNI:
- Plug the desired device into the black fiber-optic connector on the right side of the front of the magnet bore
- Locate the silver box (labeled fORP) in the control room to the right of the GE console.
- Push in the knob on the right front side of the fORP box to enter menu mode. For the following instructions, you will turn the knob to scroll through the menu choices, and then push in on the knob to select your choice. (See this guide for more details on using the fORP 932.)
- Turn the knob until the word "yes" is underlined then push the knob to select "yes"
- In the "mode select" menu that appears next, select "manual config"
- In the response device menu, turn the knob to scroll through the choices until you find the device that you connected in step 1:
- 4-button cylinder: select HHSC-cyl-5
- bi-manual 4-button keypads: select HHSC-2x4c
- scrollwheel: select HHSC-SCRL1
- Select USB in the next display by pushing in the knob.
- Select the desired output mode. For the cylinder or keypads, this determines the mapping between the buttons and the keypress that is generated. E.g., HID-NAR-12345 will map the 4 cylinder buttons to the four number keys, 1-4. NAR means "no auto release". In NAR mode, the keypress is maintained as long as the button is pressed. In the non-NAR mode, a brief keypress is generated, even if the button is held down. We find that NAR mode works better with PsychToolbox. In non-NAR mode, it can miss the very brief keypresses produced by auto release. For a description of other modes, see the Current Designs support site.
- Setup is now complete.
Eye Tracker
The current eye tracking system is the MReyetracking system from Resonance Technology. The eye camera and IR source mounts to a silicone eye piece that can replace the silicone eye piece on the goggles to do eye tracking with the goggles. You can also use this camera and eyepiece as a standalone eye tracker for use with the flat panel display.
The eye camera video is processed by ViewPoint from Arrington Research. This software is running on the Dell computer that sits directly behind the scan operator. To position the eye camera properly, it is helpful to see the video output. To do this, start ViewPoint on the Dell and use the video switch that sits on top of the GE console computer to show the ViewPoint window on the little display that is mounted to the scanner above the subject bed.
Subject monitoring
The scanner has the standard suite of physiological measures: pulse oximetry, respiration belt, and ECG. These can be used for scan triggering. Also, the digital data from these measurements can be saved.
Several labs have asked about a video camera positioned in the bore to monitor the subject's face. We are currently investigating this.
Scan Triggers
The moment when the scanner starts acquiring image data can be controlled from the computer you use to control your experiment. To do this you need to be able to program your computer to send a pulse to the scanner at the planned moment.
There are two methods for sending the pulse. One way is from a USB line and the second is from a serial port. The notes below show how to set up the UserCVs so that the scanner listens for the trigger, and how to send a trigger pulse using either a USB port or a serial port.
Protocol configuration
TO DO: Document UserCVs for setting up triggering.
USB-1208 HID trigger
At the CNI, we have a [USB-1208] HID device from Measurement Computing installed and wired into the scan trigger through pin 14. This device is supported by the PsychToolbox [DAQ Toolbox]. If you have PsychToolbox configured, just plug in the USB cable labeled "Trigger" and you can send a TTL pulse to the scanner by pulsing pin 14. See the VistaSoft [StartScan] function for example Matlab code.
Serial Port Trigger
The CNI also has a USB-to-Serial port device set up to send scan triggers. Just connect the USB cable labeled "Serial Trigger" to your computer. You might need to install a driver the first time you connect it. Download the Arduino Uno driver and then follow these instructions. The device is expecting communication at 57600 bps. The scanner is triggered by sending this string (without the quotes): "[t]". In e-prime, you need to add the serial port device to your experiment and then configure it (usually com 4, and be sure to set the baud rate to 57600). In your script, add in-line code to send the trigger string to the port: Serial.WriteString "[t]".
Subject Positioning
There are many MR-safe pads available for subject positioning. (Add positioning advice?)
Also, there is a Mag Design and Engineering bite-bar holder on the 8-channel and 32-channel coils (both built by Ben Krasnow). We will also get one built for the 32-channel coil if there is a need (i.e., someone asks). We have a 200deg water source in the control room (the Cuisinart coffee machine) and are planning to get a little microwave for heating things like bite bars and EEG electrolyte.
Some labs have expressed interest in a vacuum pillow system for subject positioning. From: Ashley Shurick (Gross lab) is familiar with the SecureVacTM Immobilization System from Bionix Radiation Therapy. The system at NYU uses a customized pillow measuring 50 x 70 cm with 12.5L of fill. However, the size should depend on the head coil used, as pillows come larger or smaller, with more or less fill. They also have a vacuum pump system to remove air from the pillow, helping prevent movement. We are currently looking int this.