3T Peripherals Guide
Updated on 9/21/12
Created By Miguel Perez
This will serve as both a new user’s manual as well as a reference guide for current users
of our Siemens 3T system. By reading through this and checking for updated versions,
you should always be in the know about the equipment located in the building, as well as
how to use it properly.
REMINDER: USERS ARE NOT ALLOWED TO CHANGE
THE CONFIGURATION OF ANY PIECE OF EQUIPMENT
OR COMPUTER WITHOUT FIRST MEETING WITH BIC
STAFF. NO EXCEPTIONS!
3T Control Room
Stimulus Computers
Function:
The stimulus computers, a PC and a Mac, are used for presenting visual and/or audio
stimuli to the subject. Their respective monitors, keyboards, mice and speakers are
located in the control room. If you bring any files with you on an external hard drive or
thumb drive, plug it directly into a USB port on the front of the computer. The stimulus
PC is loaded up with E-Prime, Presentation, and Matlab while the stimulus Mac has
Matlab with Psychtoolbox. By default, the computers should be kept off the network.
Location:
The stimulus computers (Error! Reference source not found.) are located in the control
room below their respective monitors and are labeled accordingly.
Figure 1 - Stimulus Computers
Login:
When using the stimulus computers, all users must be logged in under the BIC account
for the Mac and Stimulus PC. There are no passwords needed to log in and the accounts
do not have admin privileges. If you need something installed onto these computers in
order to do your experiments, drop me an email.
Location of Experiments:
Files should be kept in your respective lab subfolder in the Experiments folder on the
desktop of both computers.
Note: Feel free to use either the folder on the PC or the Mac or both. As of right now
there is no limit as to how much hard drive space each lab can use. When/If that changes
I will let everyone know.
Eye Tracking PC
Function:
The eye tracking PC is for collecting data using the eye tracking system, the Biopac
physiology recording system and the optical microphone. The monitor, keyboard, mouse
and speakers are located in the control room.
Figure 2 - Eye Tracking and Real-Time PCs
Location:
The eye tracking and real-time PCs are located in the control room below their respective
monitors and are labeled accordingly.
Note: While there is a dedicated eye tracking login, password “eye”, it’s also acceptable
to use the BIC login. Either one will work just fine.
Real-Time fMRI PC
The real-time fMRI PC is to be used for, you guessed it, conducting real-time fMRI
analysis. If you are interested in using the setup, contact the Bishop lab for details. The
system is not BIC property; therefore it is not maintained or managed by BIC staff.
Avotec Projector
Function:
The Avotec projector is used to provide a visual stimulus to your subject. Make sure to
sign up for a peripherals training session so you can get more information about setting
up the projector and the screen. The system receives input from the stimulus PC,
stimulus Mac, eye tracking PC and a laptop.
Location:
The actual projector itself is located
behind the magnet, facing the bore.
The visual system (Figure 3), which
powers the projector, is located in the
control room, right behind the Siemens
console
Figure 3 - Avotec Projection System
Setup:
Using the projector is mostly a straightforward process. Flip the power switch on,
located on the far right of the visual system, and the entire system will power on, then
select the proper video input settings (see below).
IMPORTANT: After turning on the projector you then have to go into the magnet room
to the back of the bore and adjust the settings on the projector to your exact
specifications. Using the stationary rulers as guides, adjust the height and position of the
projector, and then adjust the position of the screen within the bore using the colored tape
markers as guides. Once you find settings that you’re happy with, write them down!
There are no default settings for the physical settings on the projector and chances are
that other users will change things around prior to your scans. The responsibility falls
squarely on you to adjust the system to suit your specifications each and every time you
scan. If you need help figuring out the settings that work for you, send me an email and I
will be happy to help.
ALSO IMPORTANT: The default input settings for the projector are a resolution of
1024x768 and a refresh rate of 60 Hz. The stimulus computers already have these as the
default video settings. The manufacturer claims that it will not work with any other
settings, though some users have told me the opposite. My suggestion: use the factory
recommended resolution whenever possible. I can’t guarantee anything else will work.
If you end up changing them, make sure to change the settings back to the default ones
when you are finished.
Notes:
 If the three horizontal “sync” lights are green, then the video is functioning
normally. If not, verify you have the correct settings
 The projector takes about half a minute to warm up, be patient
Video Splitter & Switch
Figure 4 - Video Splitter & Switch
Function:
The combination projector video splitter and switch (Figure 4) is used for choosing the
video source that you want and where you want it to go. Each input and output is
properly labeled; so make sure you pick the correct one for your study. It can receive
input from the eye tracking PC, stimulus PC, stimulus Mac and a laptop.
Notes:
 The output goes to the projector as well as a separate monitor. This allows you to
see exactly what the subject sees while inside the magnet
 The projector video switch has VGA ports because the projector itself only
accepts a VGA input. For this reason, the stimulus computers output a DVI signal
for their primary monitors and a VGA signal for the secondary (that is sent to the
splitter)
 Hold down the button when switching the input; for about a second
 If you plan on using a laptop for your studies, make sure it has a VGA port so that
you can connect it to the projector. Or at the very least, a DVI to VGA converter
Audio Switch Box
Function:
The switch allows you to designate the audio input and the output you wish to use. All
inputs and outputs are in stereo.
Figure 5 - Audio Switch
Setup:
We are currently using four input channels and four output channels. A list of the inputs
and outputs is as follows:
Inputs
Outputs
1. Stimulus PC
1. Siemens audio system
2. Stimulus Mac
2. Control speakers
3. Laptop
3. 32 Ch. headphones
4. Audio receiver
The settings for “Output 1” determine which audio source will send a signal to the
Siemens headphones. This setting will usually remain on “1”, since the majority of the
scanner users would like to present the audio signal from the stimulus PC. The settings
for “Output 2” determine which audio source will send a signal to the Avotec
headphones. The default setting for this should also be “1.”
Note:


The audio switch is somewhat tricky to read at first glance, and even trickier to
explain in a guide! Make sure to pay close attention to the explanation of the
switch during the training session you attend.
The switch box does NOT control the normal communication between researcher
and subject, which is possible by using either the Avotec or Siemens systems
(regardless of the settings on the switch box)
32 Channel Headphones
Function:
Due to the inner diameter limitations of the 32 Ch. head coil, it is simply impossible to
use the standard Siemens headphones with it. In order to provide audio to your subjects
you must use the specified 32 ch. red and blue ear buds.
Location:
The red and blue ear buds are dangling on the left side of the face of the magnet as you
walk into the magnet room. The amplifier and equalizer are located right above the
projector in the control room.
Figure 6 - 32 Ch Headphone System
Setup:
It’s not important or necessary to fiddle with any of the components of the 32 Ch. system.
All you ever need to do is turn them on in the correct order. They are labeled as 1, 2 and
3, so simply turn them on in that order and then turn them off in reverse order when
finished. Once that’s done you must go to the magnet room and verify that the BNC
connectors for the ear buds are connected to the pin panel in the far corner of the room.
They are color coded (blue and red) so simply connect them up and the headphones are
ready for use.
Notes:
 The headphones must be unplugged from the panel once you’re done scanning.
Do not leave them plugged in.
 The system is comprised of four different components.
o Behringer Ultra-Di Pro Professional 4-Channel Di-Box model Di-4000
o Behringer Ultra-Curve Pro model DEQ2496 Digital Audio Processor
o Behringer Reference Amplifier A500
o Sensimetric MRI-Compatible S14 Insert Earphones
FORPs
Function:
The FORPs (Fiber Optic Response Pad) are used to collect responses from the subjects,
as well as deliver the TTL pulse from the MRI equipment to the computers. They
connect to the MRI compatible button response boxes inside the magnet room. We
currently have FORPs for the stimulus PC, stimulus Mac and a laptop. The
FORPs(Figure 7) are located on the shelf above the monitors in the control room.
Setup:
All FORPs connect to their respective computers through a USB cable. For the stimulus
computers, that means they are always connected and receiving responses as well as the
TTL pulse (see below). The laptop FORP connection is located on the work desk (see
below). Currently we have two FORPs connecting to the Stimulus PC (4-button and 5button) the Mac also has two (4-button and track ball) and the laptop has one 4-button.
Most users will only have need for the 4-button, but if you need to use any of the other
fORPs then please contact me so that we can go over the details.
Figure 7 – FORPs
TTL:
The FORPs also serve as the delivery method for the TTL pulse to the various computers.
Each FORP has a BNC cable connected to it that comes from the same system and
supplies the TTL pulse. Thus, it is ESSENTIAL that the FORP be plugged into the
computer at all times.
Notes:
 Make sure to coil up the response boxes properly and hang them on their
respective hooks when finished. They are easily damaged and take a few weeks to
get fixed. Damaging the cables not only effects your scanning schedule, but the
schedule of all other users.
 Output from the FORPs are reported as “1”, “2”, “3”, and “4”. They correspond to
the four colors on the boxes, starting from the left.
 The TTL pulse reports as “5”
 Each computer will recognize the FORP response as keyboard presses, so adjust
your scripts accordingly.
 The units operate independently of each other and should always be connected
and powered up

If the fORPs ever fail to register button presses or TTLs, give them a quick power
cycle. There is a simple switch (Figure 8) that you flip located to the left of the
fORPs.
Figure 8 - fORP Power Cycle Switch
Siemens Audio System
Function:
The Siemens system is the audio system we currently have set up for use. It contains
speakers INSIDE the magnet room and a microphone inside the bore (spiffy right?).
Location:
The Siemens control box is located on the
control desk to the left of the monitor and
1
keyboard.
Setup:
The Seimens control box (Error!
Reference source not found.)has several
different controls:
1. Table stop button
2. Listen button
3. Play music button
4. Speak button
5. Listen mode volume control
6. Patient instructions volume control
2
5
6
3
4
Figure 9 - Siemens Audio Box
General Use:
1. Table stop button – The table movement is stopped immediately, it also stops the
sequence you are running.
2. Listen button – Lets you listen to the subject inside the magnet. The LED should
light up when in use. Push the button again to end the transmission.
3. Play music button – This allows for audio to come in from a different source, i.e.
the stimulus computers. Push the button, have the audio switch properly set, and
audio should be directly sent to the subjects headphones. The LED should light
up when in use. Push the button again to end the transmission.
4. Speak button – Press and hold to speak to the subject. LED should light up
when in use. Also works to shut off the alarm that is triggered if the subject
squeezes the squeeze ball.
5. Listen mode volume control – Controls the volume of the patient’s voice when
they are speaking to you.
6. Patient instructions volume control – Controls the volume of your voice to the
patient’s headphones
Notes:
 An alarm is activated by a plastic squeeze bulb that the subject holds onto while
they are inside the scanner. When the subject squeezes the bulb, an audible
alarm sounds continuously on the control box until the Speak button is pressed
to reset the alarm
 Headset covers are located in the drawers by the scanner
Laptop Connections
NOTE: Before you decide you wish to use your laptop for conducting studies, please
meet with me. We have several issues that need to be discussed that you need to be
aware of before proceeding.
Function:
There are five connections that will allow you to connect up a laptop in order to provide
audio and visual stimuli. Any laptop you wish to use will require the following ports in
order to fully utilize our setup: VGA, USB, audio, ethernet and BNC(for extra TTL
input).
Location:
The cables are located on the work desk next to the projector monitor and are all labeled
to prevent confusion.
Setup:
1. VGA – Labeled “projector.” Used for providing video input for the projector. Make
sure the projector switch is set to “laptop” and you are familiar with switching the
video outputs of your laptop.
2. USB – If you intend to use the response box or need the TTL pulse in order for your
scripts to work, you will need to plug this in. It connects to the laptop FORP.
3. Audio – This will allow you to connect your laptop to the audio switch. From there
you can select the proper input channel, “3”, to provide audio to the system you
intend to use.
4. Most of you will not require the BNC to deliver TTL pulses. That’s typically reserved
for external devices that need a TTL pulse as well, but we lump it together with the
laptop connections to simplify things.
Note: If you plan on using your laptop, make sure it has a VGA port on it. Or else you
won’t be able to use it with the projector
Receiving/Testing Room
Recording Mac and DVD Burners
Function:
The recording Mac and DVD burners are used in order to make copies of scanning
sessions. Simply make a DVD of your session for yourself, hook up an external hard
drive, or use any other method you can think of to get your data moved from the scanner
building to your laboratory.
Location:
The Recording Mac, including all the related peripherals (Figure 6), is located in the
receiving room adjacent to the control room.
Figure 10 - Recording Mac
Setup:
All of the equipment that is necessary for making copies of your sessions is located by
the recording Mac. That includes: DVD-R disc, disc sleeves, a DVD-R burner, and the
recording Mac itself.
Burning a CD:
1. On the recording Mac, start the Osirix program if it's not already running
2. Open the Patient Browser on the Siemens PC, and then highlight the patient or
session you wish to back up
3. Select the Transfer menu option, and then select Send To and highlight OSIRIS
(The only option)
4. Wait a few minutes for the data to transfer
5. Move over to the recording Mac. You should see the files being transferred
6. Select the patient or session name you wish to back up and then click the Export
icon on the top menu bar. Export your files to the desktop
7. If you haven't already put a blank DVD into the external drive
8. Once you put the blank DVD in, you will be prompted with a pop up window,
click “OK”
9. Drag your data onto the DVD icon and being the burning process.
10. Let it burn. It will take several minutes, depending on the amount of data
Metal Detector
No, we did not get a new
metal detector for the
facility! Those of you who
have been around for a few
years will remember it
from the 4T building before
the Siemens 3T was
installed. Feel free to use
the metal detector to verify
that your subjects have
removed all metal from
their person before entering
the magnet room.
Figure 11 - Metal Detector
Testing Computer
Figure 12 - Testing Computer
The testing computer is located in the back cubicle and is loaded with E-Prime, Matlab
and Presentation. It also has a USB button box attached to it. There are currently two
purposes for the computer: one is to train your subjects on the task they will be
performing while inside the magnet, and the other is to conduct behavioral testing either
before or after their scan.
Magnet Room Supplies
Inside the magnet room you will find several MRI-safe shelving units. Inside them you
will find most of the supplies you need in order to scan and make your subject
comfortable. This includes:
1.
2.
3.
4.
5.
6.
7.
8.
Foam pieces
Cleaning wipes
Ear plugs
Vitamin E capsules
Medical tape
Lens cleaner and wipes
Blankets
Headphone covers
Most disposable supplies will be stored here, with the exception of the pregnancy test.
Pregnancy tests are kept in the storage room! Remember that all women must take a
pregnancy test BEFORE stepping inside the magnet room. Please let me know if you
need any other disposable supplies that are not already available for use.
Note: If supplies run low, check the storage room before emailing me. The room is
located adjacent to the 3T operator room. The key can be found on an aluminum rod by
the Siemens console.