MRI Equipment

Scanners

Siemens Skyra 3T

The Siemens Skyra 3T has Syngo MR VE11c software (as of Nov 14, 2018). 7 new licenses have been installed (3D ASL, Abd Dot, Freeze IT, Liver Lab, Multiband, MyoMaps, Resolve, SMS). In addition, several WIPs (beta sequences) have been updated to work with the new VE11C software. A 32 channel head coil and a 20 channel head coil are available.

Siemens Cima.X 3T
Some differences between the Cima.X and Skyra are listed below:

• The Cima.X has much stronger gradients (200 mT/m) compared with the 3T Skyra (40 mT/m) and therefore can scan somewhat faster and provide improvements in SNR for several sequences, most notably diffusion MRI.

• There is a 64-channel head and neck coil on the Cima.X as well as a 32-channel head coil (identical to the one on the Skyra).

• The Cima.X is running XA61 software which has new capabilities compared to XA30 on the Skyra.  It is still XA software, so the interface is the same.

• The magnet bore is 60 cm diameter which is smaller than the Skyra (70 cm).  Subjects will be snugger than on the Skyra.  The bore is the same as 3T Prisma if anyone has worked on that system.

Siemens Freemax 0.55T

This is a smaller machine, especially useful for body imaging.

Please treat all the equipment carefully! This equipment is a shared resource that is used daily (and sometimes nightly) by multiple labs. The equipment is highly specialized and, therefore, very expensive, and many components and cables are fragile.

We have tried to set the computer and the equipment up in a way that will work for everyone. If there is anything that doesn't work or that could be set up better, please get in touch with Heidi Elledge or Scott Squire, the head MRI technicians.

In general, someone who weighs over 300 pounds and is not that tall probably will not fit comfortably in the bore.

You are expected to abide by the TBIR Code of Conduct.  Please read it.

Download a copy of the MRI screening form.

Data Transfer

Data can be transferred from the scanner over the network.  The IP address of the scanner has not changed (same before and after the move).  See Horos Setup for information about setting up Horos for the mac. Alternatively, you can copy data onto a USB drive (the top USB slot in the console computer is USB 3.0)

Facility Access

To access the MRI scanner, you need to (1) Complete Safety Training & CPR  and (2) Request access to BSRL (the building).

Generally, BSRL building access is Mon-Fri 6 am to 6 pm for most researchers, but you need a PIN before 8 am. After you have been approved for access, use this University URL to get a PIN:   https://www.fm.arizona.edu/DACPortal/index.html#/SelfAccess.  Note that you need to keep track of your PIN, since the website does not display your current pin.

If you encounter access problems, please contact Andy Rouse (rouse at arizona.edu).

Physical Access 

The official address of the building is:

Bioscience Research Laboratory
1230 N Cherry Ave.
Tucson AZ, 85719
Scanner Console Phone: 520-626-2542

iLab Scheduler

If you are a PI, you need to ensure you are signed up to use the iLab scheduler site before members of your lab can get access. Here are instructions for working with iLab. If you encounter difficulties getting iLab to accept your account number, contact Andy Rouse (rouse at arizona.edu). 

To reserve scan time using iLab: 

• Login to your iLab account

• Click on the "Memberships" drop-down at the top of the page

• Select "My Groups" (on the left) and then select the desired lab

• Open the Membership Requests & Account Numbers tab

• Scroll down (towards the middle of the page) to a section where you can select your account number.

• Enter the account number to charge for the scans.

If you are not a PI, you can still sign up to use iLab. On the iLab site, select a PI and that PI will get an email asking them to add you ( this assumes your PI is in the system). Once you are in the iLab system, other PIs you work for can add you and you will receive a confirmation on iLab (not an email). You'll see these notifications under Home->Communication on the left of the iLab page when you log in.

The iLab scheduler is available from anywhere (you don't have to be on the UofA network to access it).

Consulting / Testing Rooms

Rooms 73 and 74 (reserve in iLab) are the original square carpeted consultation rooms.

Room 50 (reserve in iLab) is accessed via a short side hallway across the hall from 73 and 74. Room 50 is larger than the other rooms and has a sink.

Room 54 (walk-in) is off the wide hallway that becomes the 3T console space but on the south side of the double grey doors. It is rather small and narrow, but it will work for most projects.

Usage Policy and Directions:

• There is no charge to use these rooms.

• The rooms are only available to investigators interacting with participants that will, at some point, be scanned on the 3T (that scan can be on another day).

• Please leave the door open when not in use. Do not leave the doors closed with “IN USE” tag hanging from the doorknob when the room is not in use.

• Please minimize unnecessary reservations and last-minute cancelations.

• Reservations must be made more than 8 hours in advance. Any open time slot you see for the current day is considered walk-in because it can no longer be reserved in iLab.

• All rooms share the same iLab calendar. Just open the “Consultation Rooms” calendar, drag a reservation time slot, and choose your room near the top of the reservation info screen. (See Figure 1 below).

• The calendar doesn’t differentiate rooms at first glance. Hover over a reservation to see the room number for that reservation. Multiple room reservations for the same time slot will be stacked graphically on the calendar. If you see three reservations for a given time slot that means all three reservable rooms are booked. (See Figure 2 below).

Required Safety Training

(1) Safety training is available through D2L. Your PI should have access to the D2L site to sign you up for training.  If not, contact Dianne Patterson: dkp @ arizona.edu.  You will be expected to watch a video and take a quiz.  When you have finished these online activities, you'll need to arrange to visit the facility so you can ask questions, ensure you know where everything is, and get your final approval from Scott Squire or Heidi Elledge (the MRI technicians). During your visit, you can request building access from one of the technicians.

(2)  You will be expected to complete Heartsaver CPR training as well, and to maintain that certification. More details are available on the Safety Training & CPR  page. You can request building access before you complete this.

Peripherals

Console PC

HP Z400 workstation with Windows 7, USB 2.0 and 3.0 and firewire 400 ports in front. USB can be used for exporting data to a key/hard drive.

The PC in the corner of the scanner console room is used for presenting stimuli and collecting responses:

Lenovo ThinkStation S30

Processor: Intel Xeon E5-1620 3.6 GHz quad core

Memory: 4 GB RAM

Video card: NVIDIA Quadro 600 with 1 GB RAM

Audio card: Creative Sound Blaster SB1270 X-Fi Titanium HD with THX

Operating system: Windows 7 Professional, 64-bit

Monitor: ThinkVision LT2452p 24" 1920 x 1200 LED

Update: May 31, 2018: Rebuilt the Task PC: 

DMDX 5.1.2.1

Eprime 2.0.10.353 SP1 (201)

Matlab 2012B 

DirectRT: Broken

User Accounts: The user account "mr4-user" is intended for general use. The password-protected account "mr4-admin" is an administrative account. Labs that would prefer to use their own account rather than the generic one should let Scott Squire know and he will set one up.

Task Files: Please save your task files under C:\Experiments in a folder labeled with the PI and optionally the year (e.g. for Dr. Plante: Plante_2014, Plante_2016_Russian, Plante_2016_NAD2, etc.).  Feel free to place a shortcut on the desktop. The goal is two-fold: 

1) Get everything into a folder that will be easy to back up.

2) Ensure that we can identify old studies (by adding the year) that could be cleaned off if we need more room.

Please don't change the video or audio settings on the computer. In particular, the audio volume should not be changed on the computer. Instead, the amplifier/mixer (see below) can be used to adjust the volume and source.

Use Your Laptop for Stimulus Presentation

Many researchers prefer to use their own laptop for stimulus presentation.  The advantage is that you know exactly what the presentation program settings are, exactly how the timing will behave.  You need to connect your laptop into the system with the appropriate connectors shown below for the button boxes, sound, and video.  Generally, programs see the USB button boxes as keyboard input, but check your program to make sure.

In addition to plugging in your laptop, you need to set the ATEN device (pictured below) to Laptop mode by pushing the number buttons on the front until all the lights are on side 2. Please reset the ATEN device when you are done so it always defaults to the Task PC:

Auditory Stimuli

Sound Mixing

The ROLLS MA251 amplifier/mixer (Rolls MA251) sits on top of an ATEN switcher (pictured below). The volume of each channel can be adjusted to control the connected device. Except for the microphone (channel #1), all audio is output to the Sensimetrics headphones. The channels are numbered (weirdly) right to left on the device. Reading left to right:

Channel 4 laptop: Audio input from an optional laptop. 

Channel 3 Stim PC: Audio input from the Task PC sound card.

Channel 2 Music: Audio input from an auxiliary audio plug (e.g. music from a phone).

Channel 1 MIC: (FOMRI III MR Microphone) Audio feed from the participant in the scanner. (The MR compatible noise cancelling microphone is described in more detail below).

FOMRI III Dual Channel Microphone System for fMRI

If you want to record what a participant says in the scanner, you can use this specialized microphone from Opto Acoustics. Microphone Specifications and User Manual available. Use channel 1 on the Rolls MA251 to control audio from the microphone volume. You can use any recording program but the microphone comes with specialized software (optiMRI) to optimize speech and minimize scanner noise.

The microphone records three channels: 1) the voice and the scanner noise, 2) just the scanner noise and 3) real-time, noise-canceled voice data.

All microphone outputs are attached to the Task PC. Microphone channels #1 and #2 (above) connect to USB ports 7 and 8 as Microphone (USB Audio Codec). There is also analog output for channels #1 and #3. The scanner noise channel (#2 above) is not connected to the Task PC sound card.

To use Audacity, set the speaker to Realtec Audio speakers and the microphone to any USB Audio CODEC. The optiMRI software can do better than Audacity, but there are some issues in getting the stimulus presentation to call the program automatically. 

Button Box Response System

Participants' responses are collected with Current Designs button boxes. We have package 904.  The boxes use fiber optic cables (handle with care!) which connect to the interface box in the control room.  Depending on how this interface box is set, it may or may not collect each of the unique signals associated with your device. 

For the pair of button boxes shown above, the four buttons are mapped as follows:

• Blue = 1

• Yellow = 2

• Green = 3

• Red = 4

To test this common configuration, open Notepad on the Task PC. Then, press each button on the button boxes. The mapped numbers should appear in Notepad as they are sent from the button boxes.  You can expect the same color-digit correspondence for the other button boxes.

If only a subset of numbers appear, then push the dial on the silver interface box and turn the dial to select: Mode Select->Autoconfig->12345. Now the button boxes should work correctly.

The button boxes should be treated with care and coiled up on the hook on the wall when not in use.

Finally, there is a writing tablet and MR compatible pen.  This acts just like a mouse; so that touching the pen to the tablet and lifting it off again can easily be registered by a program like Eprime.  The primary goal of using the tablet is to detect when participants are engaged in writing or drawing, but not what they are writing or drawing. However, if you open MS Paint and have the participant double tap the pen on the tablet, then it is possible to draw.  Right now, this appears backward (mirror-image) to the participant. The tablet is described in this article: Tam, F., Churchill, N. W., Strother, S. C., & Graham, S. J. (2008). System for computerized writing and drawing during fMRI. Proc Intl Soc Mag Reson Med, 17, 1703–1704.

Scanner trigger

At the start of each functional volume, the scanner sends a TTL pulse which feeds into the Current Designs interface box, and is read by the Task PC via USB as a "5" keypress. One pulse is sent every TR. However, note that pulses are not sent for the initial obligatory dummy volume(s). So the first pulse will coincide with the first volume that is actually retained. Any presentation program that can be triggered by the "5" key can be started automatically by the scanner and, thus, perfectly synchronized.

Eye Tracker Setup

Eyelink 1000 eye tracker equipment

See the detailed specs.  This is an eye-tracking system with a fiber optic data transfer cable designed for the scanner (the data transfer cable is orange).  There are two black power cables with identical connectors.  The one marked with tape plugs in to the camera.  The other plugs into the illuminator. The stand shown fits in the bore (there are some marks on the bore, in black sharpie, to help you place it correctly).  When placed in this location, it is largely buffered from scanner vibrations.  Make sure that the illuminator is on the same side as the eye you want to track to avoid shadows cast by the head coil.  The distance from the camera to the eye is ~127 cm, so the camera and illuminator should be adjusted so each is centered on ~127 cm marks on the horizontal mounting bar. You can minimize the effects of the head coil shadow by raising the participant's head as close to the bars in the head coil as possible, and requesting that the participant move their eye so it is centered in the most open space (but still allowing them to see through the untracked eye).  The device is currently set up to track the left eye because this allowed us to orient the delicate cables medially rather than having them jammed against the bore.  Moving the illuminator forward or back can significantly affect the success of eye tracking.  Once you have positioned the illuminator, make sure you lock it down with the screws on its underside.

Eye-tracking Computer Setup

Turn on the Eyelink computer (small black computer pictured below) and you should see a command prompt.  If the camera is correctly plugged in, it should auto-detect and start the graphical interface. If not, press "t".  Have the participant hold a finger beside their left eye so you can determine which eye to focus on. The left eye will appear on the right side of the screen.  Use the arrows (--> and <--) to zoom in and out of the tracked eye.

The Eyelink computer is connected to the Task PC by a yellow ethernet cable.  This transfers data between them. Ensure the two computers can communicate via the ethernet cable:  

• On the Eyelink computer, click the network card icon. 

• Select Properties--> TCP/IP. 

• Select "use the following IP address: 100.1.1.2. 

• Enter the subnet mask 255.255.255.0.

If the networking between the two computers is correctly configured, Python code running on the Task PC can synchronize with the Eyelink system. Once your Python program is started on the Task PC, you should be able to hit "enter" on the Eyelink computer and clone the Eyelink screen to the Task PC.  This can help researchers in the scanner room to adjust camera position and focus, because they can see the stimulus presentation. 

Both VisionEgg (a Python library for presentation) and Matlab are on the Task PC. In addition, the Eyelink computer includes a program called Experiment Builder which can be used to facilitate writing Python code. 

Inter-Pupillary Distance

About half of all participants will have their eyes partially occluded by the 32 channel coil.  The more occluded their eyes are, the more the  image of their eye will jitter, making eye tracking unreliable or even impossible.  The 20 channel coil solves this problem, but seems to have roughly 1/3 of the SNR.  Interpupillary distance may be the critical factor in eye occlusion.  Interpupillary distance is typically 60-67 mm.  Mine is 58 mm and we cannot track my eyes in the 32 channel coil (see picture below).  The greater the interpupillary distance, the more visible the eyes are for eye tracking. In the best case, the entirety of each eye should be visible.  As less eye is visible, the tracking becomes jerky and irregular until tracking is erratic or impossible.

Measuring inter-pupillary distance: It "should" be the case that you measure from the inside of one pupil to the outside of the other pupil. However, at least, with the calipers, it worked better if we measured from the outside of one pupil to the outside of the other. Here "better" means the resulting values were more consistent with expected values from the optometrist.

In our experience, introducing corrective lenses for the participant also makes eye tracking much more difficult.

Safety equipment

The Transcranial Magnetic Stimulation (TMS) Laboratory 

The TMS lab includes a MagVenture MagPro X100 stimulator (MagVenture Inc. Denmark), 3D Neuronavigation system (Localite TMS Navigator, Germany), and Electromyographic system. To learn more, contact the lab director: Ying-hui Chou yinghuichou at  arizona.edu. More information about the equipment is available here.