Introduction

Usage

MRI is ideally suited for real-time monitoring of ongoing brain activity. The LIBC MRI scanner is equipped with all necessary facilities to perform MRI studies suited to answer a broad range of cognitive neuroscientific research questions. For example, you can use the MRI compatible headphones for auditory stimulation and the BOLD screen to present high quality visual stimuli inside the scanner. Button response boxes can be used to record manual responses during scanning. 

More facilities

Close to the MRI scanner two interview rooms are available for pre- and post-testing of your participants. Collected MRI data can be uploaded to the advanced computational infrastructure for neuroimaging analyses. The LUMC also hosts a special dummy scanner. This scanner is mainly used to familiarize children with the research setting.

Training

The LIBC support team ( supportlibc@lumc.nl, LIBC fMRI Research website) can provide expertise in all phases of your project. You will be extensively trained for safe and independent use of the LIBC MRI research equipment

Support

For support regarding the LIBC scanner, please contact supportlibc@lumc.nl, or visit their the LIBC fMRI Research website.

Setup Overview

The LIBC has a 3 Tesla Philips Achieva dStream MRI scanner located in area J0-53 of the LUMC. To aid in human research, the setup features additional peripheral hardware and software for participant interaction. These software and hardware additions are supported by SOLO together with the LIBC MRI technicians.

The scanner control room features two stimulus presentation PCs running a variety of research software, such as MATLAB, E-Prime, and PsychoPy. Additionally, the following research equipment is available for use with participants in the MRI chamber:

• 32 inch monitor (CRS Ltd. BOLDscreen32).
• headphone-based audio stimulus delivery system (MR-CONFON).
• Eye-tracker (SR research EyeLink 1000).
• BIOPAC with EDA module.

MRI-participant responses are collected via two four-button button-boxes and transmitted as keyboard keystrokes to the stimulus PCs. Similarly, the scanner can be configured to sends keystrokes to the stimulus PCs at key events during its scanning sequence, which can then be used to sync the stimuli with the scanner.

The setup features various video, USB and LPT switches, which allows various researchers to use the peripherals in different configurations without having to disturb the arrangement.

Do not modify any part of the setup without explicit approval from the LIBC technical support team. Also, do not use any device without prior approval from the LIBC technical support team.

For support regarding the LIBC scanner, please contact supportlibc@lumc.nl, or visit their the LIBC fMRI Research website.

Stimulus PCs

The current setup consists of the (old) Win7 and the (new) Win10 stimulus PCs. These PCs are connected to the rest of the setup by means of USB and video switches, allowing users to select which PC they want to use without disturbing the setup.

Both stimulus PCs are connected to the BoldScreen (located in the scanner room) via the BoldScreen video switch, and to the two vertically stacked monitors via the clone and desktop video switches. When using the stimulus PCs, the top monitor (“clone monitor”) displays a clone image of what the participant sees on the BoldScreen; the bottom monitor (“desktop monitor”) displays the main desktop.

The USB peripherals (keyboard, mouse, fORP box, E-Prime dongles, etc.) can be switched between the Win7 and Win10 PCs using the USB switch. The eye-tracker is connected to both PCs by means of a local network, so no manual switching is required. The MR-CONFON system currently only has a single input, and the 3.5 audio input is connected to the Win7 PC but can be moved to the Win10 PC or an external music device if necessary.

The Win10 stimulus PC features the standard LUMC operating system, and has internet and LUMC-network access, whereas the Win7 stimulus PC runs a standalone Windows 7 operating system without network or internet access.

Switching Between Stimulus PCs

The monitors and peripherals can be switched between the Win7 and Win10 PCs using the USB and video switches. Additionally, the switches can be used to connect a laptop to the BoldScreen and the USB peripherals.

• To use the Win7 PC:
  • Set the USB switch to A.
  • Set the clone and desktop video switches to 1.
  • Set the BoldScreen video switches to 1.
• To use the Win10 PC:
  • Set the USB switch to B.
  • Set the clone and desktop video switches to 2.
  • Set the BoldScreen video switches to 2.
• To use a laptop:
  • Set the USB switch to C.
  • Set the BoldScreen video switches to 3.

Please always leave the setup in the Win7 PC configuration when done.

Software

The Win7 stimulus PC features the following software packages:

• MATLAB 2012B with PsychToolbox (incl. GSTREAMER). The MATLAB license includes the Statistical Analysis and Data Acquisition toolboxes.
• E-Prime 2.0.10.356 (Professional).
• E-Prime 3.0.80.
• PsychoPy 2.
• OpenSesame.
• NeuroBS Presentation (license managed by Mischa de Rover).

The Win10 stimulus PC currently features the following software packages:

• MATLAB (LUMC license) with PsychToolbox and GSTREAMER.
• E-Prime 3.0.80.
• OpenSesame.

InterviewPC_1 (2022)

• OpenSesame 3.3.12
• Psychopy 2022.2.4
•  

Note that since the Win10 PC has an internet connection, online experiments—like those hosted on Gorilla, Pavlovia or JATOS—can also be used. Users generally do not have admin privileges on neither Win10 PC nor Win7 PCs, please contact the support team if you require additional software (supportlibc@lumc.nl).

NOTE: the license dongles for E-Prime are located in the USB-hub behind the monitors.

Experiment Storage

On both PCs, a local folder (C:\ExperimentData\) is provided where users can save and run their tasks. Please put your files in a project-specific subfolder using the following convention:

C:\ExperimentData\<ProjectCode>\

where <ProjectCode> is replaced by the unique 5-letter project code.

Note that data on the C drive does not have a back-up. Meaningful changes of your task/code should therefore also always be saved somewhere else.

Stimulus PC Settings

Both the Win7 and Win10 PCs should have the same general settings: the NVIDIA Quadro K2000D should produce the cloned images for the BoldScreen and the clone monitor. The main desktop image is produced by the other video card. The mirroring of the image for display on the BoldScreen is done by the BoldScreen itself.

On both PCs, if for whatever reason the main desktop changes to the wrong display, change it back by opening the NVIDIA Control Panel (right-clicking somewhere on the desktop), navigate to ‘Set up multiple displays’, and use the screen icons to the set the primary display (right clicking the icons opens a menu). The primary display should be the one that corresponds to the bottom monitor.

Researcher-Supplied Stimulus PC (BYOD)

User-supplied PCs or laptops can be used if the stimulus PCs do not meet the research requirements. To use a laptop, connect it using the cables behind the stimulus PC monitors, and set the switches to the following states:

• Set the USB switch to C. This gives the laptop access to the keyboard and mouse, the fORP box (and hence the scanner triggers), the E-Prime dongles, etc.
• Set the BoldScreen video switches to 3. This gives the laptop access to the BOLDscreen.
• Laptops cannot make use of the clone and desktop monitors.

Stimulus PCs Video and USB Diagram

The two stimulus PCs are connected to the BOLDscreen and the desktop monitors via video and USB switches, allowing easy switching between the two PCs. Additional cables connecting to the third ports on the BOLDscreen and USB switches are available for a researcher-supplied laptop (BYOD). These cables give access to the BOLDscreen (via DVI/HDMI); and the mouse, keyboard and E-Prime dongles (via USB).

The stimulus PCs are also connected to an audio system and other peripheral equipment. See below.

BOLDscreen

The BOLDscreen is an MRI compatible TV screen used to present visual stimuli to the participants. The screen is manufactured by Cambridge Research Systems.

BOLDscreen Specifications

 The BOLDscreen32 can only be driven in three video modes:

• 1920 x 1080 @ 120Hz
• 1920 x 1080 @ 100Hz
• 1440 x 1080 @ 100Hz

On the stimulus PCs, when tasks are set to run lower resolutions, such as in E-Prime, the PCs video card automatically scales the video output so that it is compatible with the BOLDscreen.

The BOLDscreen’s active viewing area measures 31.55” diagonally (698.4 mm by 392.9 mm, with a 0.36375 mm pixel pitch). The screen is set to maintain a brightness of 120 cd/m² and features typical a grey-to-grey response time of 5 ms.

BOLDscreen Viewing Dimension

Participants lying in the scanner see the BOLDscreen via a mirror mounted above the head-coil. The BOLDscreen is located behind the scanner, superior to the participants head. The distance from the participant’s eye to the mirror is approximately 9 cm. This distance depends on the participants head size and cushioning.

1. The distance between the mirror and the BOLDscreen is approximately 198 cm. This was measured using the following procedure:
2. The participant table was moved until the red alignment laser was aligned with the lateral corner side of the eyes.
3. The position of the red laser light on the head coil was marked.
4. Using ‘Go to scanplane’, the participant’s head was moved into the middle of the scanner.
5. The BOLDscreen was positioned behind the scanner using the red alignment tapes on the floor.
6. Lastly, the distance between the BOLDscreen and the marker on the head coil was measured.

BOLDscreen Troubleshooting

If the BOLDscreen does not turn on, or show the desired image, perform the following checks:

1. Verify that all the image source (e.g. the Stim PC) is turned on and logged in.
2. Make sure that the remote-controlled power socket (in the technical-room) is plugged in, and turn it on using the BOLDscreen remote. This should provide power to the BOLDscreen.
3. Make sure the DVI video switches are set appropriately, see the Stimulus PCs section.
4. Verify that the stimulus PC is detecting the BOLDscreen, and including it in its video output. This can be done by right-clicking the desktop and launching the Display Settings dialog window. Also check if the output is at a resolution and refresh-rate supported by the BOLDscreen:
   • 1920 x 1080 @ 120Hz
   • 1920 x 1080 @ 100Hz
   • 1440 x 1080 @ 100Hz
5. If the BOLDscreen still does not connect, or if it does connect but fails to show the image properly:
   1. Turn the BOLDscreen off using the remote.
   2. Make sure that the SD card on the back of the BOLDscreen is properly inserted (do not insert or remove the SD card when the BOLDscreen is on).
   3. Reset the DVI video switch by switching it to ‘4’, waiting 3 seconds, then switching it back to ‘1’. If that doesn’t work (after step 4), hard-reset the DVI video switch by removing its power momentarily (temporarily unplug the power-cable on the back of the DVI video switch).
   4. Turn the BOLDscreen on again using the remote.

BOLDscreen Health & Quality Check

The BOLDscreen 32 system was purchased in 2017 from Cambridge Research Systems Ltd. https://www.crsltd.com

The model that we have is no longer in production, and as parts are becoming sparse, the possibility for repairs in the future will become very limited. To have some insight regarding the current health of the BOLDscreen (catastrophic failure not included) regular quality checks can be performed. To do this:

1. Turn on the BOLDscreen and display a uniform white screen from the stimulus pc, for ~30 minutes. Then turn both off
2. Turn the BOLDscreen back on, but do not turn the stimulus PC on.
3. A status view should appear on screen
4. Take a photo of the screen
   
5. Send the photo to the Cambridge Research Systems support support@crsltd.com and ask them to check it for irregularities.
6. Note: for accurate luminosity and color readings an external light/colorimeter should be used.

Button-Box and Scanner Interface

Participants can interact with tasks running on the Win7 or Win10 stimulus PCs using the button-boxes, which send optical signals to the fiber Optic Response Pad (fORP) box, which in turn translates the button presses into keystrokes. In the default configuration, the buttons are mapped to keys 1 to 4 (right hand, index to little finger) and to keys 6 to 9 (left hand, index to little finger). The button boxes are type HHSC-2x4-C, manufactured by Current Designs.

The scanner sends TTL pulses to the fORP box via the thin BNC cable, which the fORP box then translates into keystrokes with the value “5”. If you are experiencing errors with the fORP box, restart it by temporarily removing its power. The fORP box supports the modes listed below.

Mode 001 is the normal operating mode at the LIBC scanner, please always leave it set to 001 when done.

Syncing a task with the scanner

The scanner can be configured to send a trigger at the start of the scan sequence. This is set in the exam card. In the default configuration, the fORP translated this trigger to a keystroke of the character "5". As such, the standard procedure is to have the task pause at a "waiting for scanner" object, which is terminated when the 5 is received.

Grip Force Measure

There is also a Grip Force device that can be attached to the button press box. If you are interested in using this device, please contact supportlibc@lumc.nl and labsupport@leidenuniv.nl. See also here for a use-case example.

Audio Systems

The scanner consists of two separate audio systems: the Philips intercom communication system, and the MR CONFON research-grade MRI headphones system.

Philips Intercom

The Philips intercom system is the scanner's built-in audio system. Consists of Philips-branded headphones connected to the scanner, and can be controlled via the intercom console and the user interface on the scanner. The system is used to speak to participants in the scanner and people in the MRI chamber, and can also play music, which the system receives via the Philips radio. Due to insufficient dampening and sound amplification, the system cannot be used to deliver clear audio stimuli during scans. Participant's voices can also not be discernibly recorded during scans.

MR CONFON

The MR CONFON system is auditory stimulus delivery system. It consists a amplifier and control unit located on the control desk, and a pair of participant headphones. It can be used to deliver audio stimuli or music to participants, and has enough sound dampening and amplification to be used during a scan. The system also consists of a desk microphone, which can be used to talk to participants through their headphones, but not people in the MRI chamber.

The MR CONFON headphones use the scanner's magnetic field to operate and therefore only work inside the bore, or in close proximity to the scanner.

Setting the volume

From the manufacturer: The maximum SPL of the HP VS03 headphone is 118dB. However, because it’s a closed ear defender and not an open HiFi system, the SPL depends on the pressure of the ear rims to the skin, i.e. the volume inside the ear defender. This effect is frequency dependent and varies the SPL by about plus/minus 3dB, especially for frequencies below 500Hz.

So, it’s a good idea to assume 120dB max SPL. This SPL is achieved, when the amp is set to 0dB gain and the output level of your sound card is set to maximum (=100%) , and the recording level of your sound file is 0dB, too.

All other values can be calculated by simply adding up the gain of the amp and the level of your sound source.

Let’s assume the volume is set to 100%, the average level of your sound file is e.g. -18dB, then you have to set the gain of the amp to -12dB to get 120dB + (-18dB) + (-12dB) = 90dB.

So far, the firmware of the amp does not offer setting of upper or lower limits. But this will become available soon. We will keep you informed.

Audio Diagram

Audio Diagram

Other Peripherals

In addition to the audio and video stimulus systems, the setup also contains an Eye-Tracker, a BIOPAC and a BNC interface for triggering external equipment.

Please contact supportlibc@lumc.nl for more information about the systems mentioned below.

Eye-Tracker

The standard LIBC setup contains an SR-Research EyeLink 1000 eye-tracker. The eye-tracker system consists of a host PC (henceforth ‘eye-tracker PC’) and an MRI compatible IR-camera that records the participants pupil(s). To use the eye-tracker PC, connect its keyboard, mouse and monitor using the extension cables behind the stimulus PC monitors. The eye-tracker keyboard, mouse and monitor should always be kept stored in their dedicated box located in the first interview room when not in use.

The eye-tracker PC is connected to both stimulus PCs via a network switch, and can thus be used by both PCs. The general installation procedure is given below (this has already been done on both stimulus PCs):

When connecting an EyeLink eye tracker to a Display PC, note the following:

• You must have an Ethernet port in the Display PC.
• After connecting the EyeLink eye tracker to the PC, setup a fixed IP address (see also the User Manual):
  • Go to: Control Panel > Network and Internet Go to: Control Panel >Go to: Control Panel > Network and Sharing Center.
  • Click on the Ethernet connection to which the EyeLink PC is connected and go to Properties (note: you need admin rights for this).
  • Select Internet Protocol Version 4 (TCP/IPv4) and click Properties.
  • Select Use the following IP address:
    • IP address: 100.1.1.2
    • Subnet mask: 255.255.255.0
  • Click OK and close all windows.
• Install the Developer’s kit. When the Developer’s kit is not installed and E-Prime task for example will give an error. In E-Prime, the IP address needs to be set to 100.1.1.1 (see sample tasks).

Note that the Win10 PC was given the IP 100.1.1.3 instead of the standard 100.1.1.2. The developers kit is pre-installed on both stimulus PCs in the following location, which also contains samples:

C:\Program Files (x86)\SR Research\EyeLink\

BIOPAC

The Biopac is located in the technical room, on the right side, close to the wave guide, and can be connected to an AcqKnowledge laptop via the dedicated ethernet cable in the control room. Note: the BIOPAC setup is still in development and is currently only suitable for EDA recording.

When you want to use it:

1. Make sure it is turned on, by pressing the power button on the back. Green lights on the front should then turn on.
2. In the control room. Make sure the BIOPAC ethernet cable (to the left of the stimulus monitor) is attached to your Aqknowledge device (e.g. a laptop).
3. Check whether the BIOPAC lpt cable is connected to the black usbparmarker device (on the right of the stimulus monitor).
   
4. Make sure the USB Switch is set to the right device (i.e. the stimulus presentation computer or laptop that you are using to present the task and send the markers).
5. To use with E-Prime, the E-Prime markers package can be used. For more information and sample tasks, see the Github page. Run a sample task (e.g. C:\ExperimentData\0. SOLO\MarkerSerialPortExample.es3), to see if the markers are being sent correctly. You should see lights on the usbparmarker device turn on. If no lights are turning on, please check if the correct COM port number has been set in the experiment.
6. Get the box labeled BIOPAC from the cabinet in the interview room. It contains the leads you will need for EDA (the short leads LEAD108B). Dry electrodes (use electrodes from an open bag first), the bag should say EL509 Disposable Dry Electrodes. And tubes of electrode gel (GEL101A). ALWAYS check the expiration date of the electrodes on the bag, do not use if past expiration. NOTE: do not attach electrodes to the leads before starting the AcqKnowledge template!
   
7. Be aware that these are dry electrodes (unlike pre-gelled BIOPAC electrodes you may have used in the past) so you will need to gel them yourself. See here for more information.
8. Start Acqknowledge, load your template or make a new one (see here for more info and here for making a marker channel). Run a test script (see step 5) again to check whether the sent markers are also being detected in Acqknowledge correctly.
9. In the scanner room, the cables come through the wall on the left side of the room (where the BOLD screen cables go through as well), they are very long and can reach to either side of the scanner bore if needed.

If you are unfamiliar with collecting EDA with the BIOPAC (inside or outside the scanner), we strongly recommend looking at the resources provided by BIOPAC (in particular Application Notes, Webinars and Video Tutorials). Some relevant ones include:

• General EDA guidelines. (Plus relevant background papers)
• EDA Guide document
• EDA FAQ
• EDA recording Webinar series
• EDA Tips & Tricks
• BIOPAC in fMRI Webinar series
• Recommended readings for Physiology in MRI 
• EDA calibration for MRI
• MRI Safety Guidelines

Some important pointers include:

• Never abrade (e.g. scrub), or wipe the skin with alcohol for EDA measurement
• Attach the two leads to Vin+ and Vin-

There is currently no protocol for using the EDA module in the scanner yet and we cannot tell you what the best settings in Acqknowledge are since no EDA studies have been done here yet. If you happen to write a protocol for your study, and or have some ideas on the optimal settings, we kindly ask you to share them with us (labsupport@fsw.leidenuniv.nl), so that we can share it with fellow researchers in turn and update the information on this wiki.

LPT Switches and BNC-Triggered Devices

Both stimulus PCs are connected to the PC LPT switch, which is used to select a PC for usage. The output of that switch is connected to the Device LPT switch, which selects which device the selected PC is connected to; this will either be the BIOPAC or the BNC isolator. The latter can be used to trigger external TTL triggered devices. To this end, an LPT-to-BNC cable is provided and connects between the Device LPT switch and the BNC isolator. This cable maps BIT7 (the MSB, which as a decimal value of 128) to the BNC plug.

Waveguides

Two waveguides are located below the desk inside the MRI control room. The leftmost waveguide is reserved for the MR CONFON headphone cables and filters. The rightmost waveguide is open and can be used for introducing non-electrical conduits, such as air-hoses and fluid-tubes, into the MRI chamber. If an electrical signal is to be introduced into the chamber, an appropriate RF filter must be used and correctly installed.

The patch panel in the technical room also features a waveguide and several pre-mounted RF filters.

Diagram

Peripherals Diagram

Exporting Data

After each scan, data should be transferred from the scanner to the LIBC archive and your personal data storage location.

For instructions, please see the manuals on the LIBC website: https://sites.google.com/view/libc-leidenfmriresearch/after-metc-approval/scanning-session/after

Please note that the LIBC archive is hosted internally in the LUMC, and is not directly accessible from the SHARK or ALICE compute clusters.

Export PACS to J-Drive

• Open WinSCP in the Desktop.
  • File protocol: SFTP
  • Host Name: sftpgw.leidenuniv.nl
  • Port number: 22
• Enter ULCN username and password then click Login (for the first time, you need to ask for access
  via https://helpdesk.universiteitleiden.nl/tas/public/ssp/content/serviceflow?unid=6c4637cd605b4ff3b474da13458d67fe
• On the left side navigate to LIBC Archive (connect it if you haven’t)
  Libc-archive$/ Brainlinks/T1
• On the right side navigate to the directory on the J-drive where you wish to store your data, e.g. under /vol/winshare/Public/ResearchData/FSW/ by double-clicking address bar and entering this path
  in the popup.
  
• You can drag and drop files from left to right.
• When you done exporting press Shift+Ctrl+D to disconnect. Then click “Close”

Interview PC's

On 14-12-2022 the InterviewPC_1 and InterviewPC_2 have been replaced with newer machines.

Old Data

Any documents that could be backed up (i.e. accessible from the common login) can be found via the Backups shortcut on the desktop. PLEASE DO NOT USE THESE FOLDERS TO STORE ANY NEW FILES!

To retrieve information stored with personal login on the old computer, follow the README in the Backups folder.

Login

This PC no longer has a common login account, you can ONLY log in with your personal LUMCnet account.
username: LUMCnet\username

Experiment Data

The ExperimentData folder is now located in C:\Users\Public\Documents\ExperimentData (there is also a shortcut on the desktop)

Remember though: this folder is NOT backed up, and is accessible to anyone who logs into this PC.
Therefore, always make sure to remove collected participant data at the end of the session/day and to keep up-to-date backups of all scripts / tasks on a safe location.

LPT Port / BIOPAC

Finally, please note that this PC does not have an LPT port (i.e. used to connect to BIOPAC or other hardware devices). If you need this, please contact SOLO labsupport at labsupport@fsw.leidenuniv.nl, as there is an USB alternative that requires a little bit of extra code in your experiment.

Software

Creating Tasks

While tasks for the scanner are run on the same software as in regular labs (E-prime, OpenSesame etc). It is important to note that they do require more specific setups, e.g. with regards to timing of the trials and jitters.

E-prime

• Introduction and Video
• Cumulative vs event timing (more details, see TIMING: Operating System Solutions.
• Eprime fmri extension: video and manual (note that we do not currently have this available).

OpenSesame:

• https://forum.cogsci.nl/discussion/298

Questions

For questions and problems please contact supportlibc@lumc.nl with CC to labsupport@fsw.leidenuniv.nl