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MR Imaging Facilities

fMRI studies are conducted on the Centre's 1.5 Tesla Siemens Vision scanner, using gradient echo EPI sequences. The scanner is operated by trained technicians from the radiology department during fMRI experiments, using preset protocols set up by BIC personnel. Some flexibility in these protocols is allowed, and you may wish to consult us on protocol decisions when planning a study.

Stimulus Presentation and Subject Monitoring

Equipment is in place for communicating with subjects in the scanner via intercom and for presenting visual stimuli or prompts using an LCD projector (NEC MultiSync MT 1030+, specifications about the projector can be found at : and mirror system. The projector runs at 1024 x 768, and can be connected to a PC, Mac, SGI, or other computer using a normal DB15 VGA cable (Macs require an adaptor which we have).

There is also an MR compatible  PS/2 mouse available.

MR Compatible Mouse and Synchronization Box

We are currently able to monitor subject feedback and provide synchronization between data acquisition and stimulus delivery software by way of a PS/2 mouse emulator. This device can be plugged into a PS/2 mouse port on a PC or SGI O2 computer (or anything else that takes a PS/2 mouse) and produces a single middle mouse button click (button down followed by button up 100 ms later) every time a scan is performed. Subject feedback from a two button MR compatible mouse is communicated as left or right mouse button clicks. Note that this device could also be plugged into a serial port. Here are pictures of the mouse connector we use (and a serial port adaptor), in case you're wondering if it's compatible with your connectors:

PS/2 Mouse Connector and Serial Adaptor

Some software for the presentation of stimuli/prompts in synchrony with fMRI data acquisition exists, but this is generally the responsibility of the experimenter. Timing of the experiment can be controlled by counting middle button clicks from the PS/2 mouse emulator, and subject feedback can be recorded by monitoring the left and right mouse buttons. There is a PC486 in the console room which is used under Linux to telnet to other machines (like an O2 in the equipment room beside the penetration panel running stimulation software) and which can also run DOS programs. If you need anything more you will have to provide it yourself at this point.

A variety of implements for subject immobilization are available, including a vacuum head cushion and a bite bar assembly. The bite bar and mirror assembly are apparatus Dr. R. Hoge built for his experiments. Because they are used by almost everybody who's doing fMRI experiments, please do not disassemble them, or if you do, please ensemble them back the way they were. The apparatus is of modular design and if parts of it are lost or broken, please let us know, so we can replace them before the next fMRI study.

Computing Resources for Data Analysis

Following an experiment, the raw data are transferred from the MR scanner computer and analyzed on the BIC computers using software tools described below. The technicians perform the data transfer, and you are responsible for telling them which node to transfer to (usually the fMRI' node). fMRI studies consume large amounts of disk space.  Because the disks on the scanner get filled quite quickly, you are also responsible for notifying the techs as soon as you have verified that the transfer was successful. It is recommended that you verify this as early as possible, because sometimes the transfers are completely or partially unsuccessful and people have lost entire sessions. The techs will delete the data after you notified them, unless you had transfer problems and they will transfer your data again.  If you don't notify the techs, data will stay on the scanner disks for 24 hours, after this period, the data will be deleted. We'd like to provide backup of the raw fMRI data on the the scanner, but this is not currently feasible. All data backup is therefore the responsibility of the experimenter.

The experimenter is responsible for data analysis, and one of the main purposes of this document is to show those conducting fMRI studies how to use the software available to analyze their data.

The following sections walk you through the steps required to plan a study, book the scanner, and do the experiments and analyze and interpret the data.

Planning The Study


fMRI studies at the Neuro have to be approved by the MNI MR Research Committee and the MNI Research Ethics Committee.

Stimulation and Feedback

You will need to work out how you are going to present stimuli or prompts to subjects in the MR scanner, as well as record any feedback that you require. Some equipment and software is in place for this purpose, but meeting specialized needs is the responsibility of the experimenter. If you plan to use your own computer for your study, there are two important facts you should take into account:
    The LCD projector used to show visual stimuli to the subject runs in 1024 x 768 mode and below. Also, if you are going to use the head coil for the experiment, it is not possible to see the entire screen area with the current coil and display setup. You should try out the display and take this into account when setting up the experiment.

    Bringing a color monitor into the MRI suite may permanently damage it, so the software for your experiment should not require a color CRT for controlling the experiment from the console room. Some people have used old color monitors.

Task Design

Subject motion must be kept to an absolute minimum, and this fact must be kept in mind when designing experimental paradigms.

Because of the stringent immobilization requirements, subjects generally can not tolerate scanning sessions which last longer than about 1.5 hours.

Booking Scanner Time

Scanner time on the Siemens Vision system can be booked through the receptionist (ext. 8510) at the MRI front desk on 3B. Make sure you book enough time to carry out all the experiments you are planning, including setup time and possible delays between scanning runs. Before you can book scanner time, make sure you have a  consent form and a requisition form, filled in and signed.
The requisition form looks like the form in the picture below:


Please make sure you fill in the Ethics Approval # and the Account #.


There are a number of safety issues to keep in mind during an MRI study. These involve various dangers posed by the strong magnetic field that exists in the scanning room.


    These are attracted to the magnet with great force, and can pose an extreme hazard. If you are in doubt about an object, ask the techs or physics personnel before bringing it into the room. Examples of potentially dangerous objects include the following: Before  you enter the scanner room, please make sure that your subject /patient doesn't have metallic clips,  metallic implants or a pacemaker, or any other ferromagnetic metal objects.

    Things which are metal but may go into the room (but not necessarily the scanner) include

      zippers and rivets on clothing (jeans are ok)

      metal eyelets on footwear

      belt buckles (still better to remove from subject or patient)

      most eyeglass frames (if in doubt, hold onto glasses when entering room - metal frames must never be used by subjects inside the scanner, as they may pose a current loop hazard)


    Where electrically conducting materials such as wires must be placed inside the magnet bore (e.g. EEG, EOG, stimulation devices), care must be taken to avoid conducting loops. The system can induce strong currents in these, and burns to the subject may result. Consult physics personnel if in doubt.

    The scanner will wipe out magnetic strip cards (credit cards, bank cards, etc.) and can damage watches. These should be left in the console room.

    The scanner may damage computer monitors. Any CRT display will be distorted if brought near the MR suites. Color CRTs in particular may be permanently damaged. LCD displays, such as those used on notebook computers, are not affected.

Carrying Out the Experiments

The usual sequence of events is as follows:

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