User Information

> MRI Safety

New Research


Scheduling MR Time

Martinos Imaging Center MRI Safety and Operations Training Manual


Table of Contents -->

1. Emergency Information for the MR Area

2. Hazards of the MR Environment

3. MR Suite Safety Rules

4. Screening Subjects for MRI Compatibility

5. MR System Operation & Safety Training

6. Running Protocols

7. Pre-scan Check-Off List [pdf]

8. Certified to Scan Check-Off List [pdf]

9. Subject Screening Form [pdf]

10. Visitor/Researcher Screening Form [pdf]

11. Acknowledgement of Reading and Understanding [pdf]




Emergency Phone Numbers

* In case of emergency call: On campus phone 100 or on an off campus phone 617-253-1212

Steven Shannon                617-324-2702 (Office)

                                      781-439-2973 (Cell)

Christina Triantafyllou         617-324-2706 (Office)

Sheeba Arnold                   617-324-2703 (Office)

Human Subject Scanning

All subjects must be given the emergency squeeze ball, and instructions on how to use it.   The subjects are to be monitored throughout the procedure via the speaker system.

Medical Emergency

In case of a human subject, an employee, or other personnel has a medical emergency, you must assist the individual out of the magnet room.   If deemed necessary call the MIT emergency line (100).

Magnet Emergency

If an individual is restrained or pinned by a ferrous object to the magnet, you must assess if the situation is life threatening.   If yes, initiate an emergency rundown to quench the magnet.

A quench includes the rapid release of cryogens and results in the loss or significant decrease of the magnetic field.   A quench should ONLY be performed by authorized personnel with proper training in dire emergency that involves a serious personal injury. Sudden loss of the magnet field in a quench situation could damage the magnet or components of the system. There is a considerable cost related to quenching the magnet and re-implementing the magnetic field. The strong magnetic field will dissipate in about a minute, releasing the individual.

Note: in extraordinary circumstances such as an earthquake or explosion, resulting in an uncontrolled quench, the oxygen level in the magnet room may significantly decrease possibly making breathing difficult.

If an individual is restrained by a ferrous object to the magnet and is NOT in a life threatening situation, call for assistance to determine the optimal way of releasing the individual from the magnetic field.   If a quench is necessary proceed as above.

Emergency Electrical Stop

If there is an emergency such as an equipment failure that could cause injury, sparking of equipment or a fire the operator or designee should immediately perform an emergency electrical stop.

Incident Reporting

In the rare event that a subject reports any untoward or unexpected reaction to the scan ( e.g. painful cutaneous sensation, nausea, etc.), the experiment is to be terminated and the incident reported to the MR Technologist Steven Shannon.   Adverse events should also be reported to COUHES using the Adverse Events reporting forms provided by COUHES . A copy of all Adverse Events reports should be submitted to Steven Shannon.

ALL incidents must also be entered in the incident log book located in the control room.

MRI Safety Website :

If a subject or patient has any medical devices, such as implants, you must get clearance from Steven Shannon. To see more information on medical devices and their MRI compatibility, please go to:



"It is not possible to prove safety, one can only disprove it." --E. Kanal, 1996

Magnetic Resonance Imaging (including spectroscopy, conventional, and fast imaging techniques) have been in use for over a decade and are viewed as medical procedures associated with acceptable and well controlled risks. Technological advances in MRI (higher static fields, faster gradients, stronger RF transmitters) have occurred rapidly, and many questions regarding the safety of these developments remain unanswered. This document provides an introduction to some of the safety concerns associated with MR research and related pages address the practical implications of these safety issues:

•  Static Magnetic Fields

•  Projectiles

•  Metal in the Body

•  Gradient Magnetic Fields

•  Nerve Stimulation

•  Acoustic Noise

•  Radiofrequency (RF) Electromagnetic Fields

•  Tissue Heating

•  Electrical Burns

•  Other Concerns

•  Pregnancy

Static Magnetic Fields:

Projectiles. The most immediate danger associated magnet with the environment is the attraction between the magnet and ferromagnetic metal objects. Ferromagnetic metal objects can become airborne projectiles when placed in a strong magnetic field. The strength of the field increases superlinearly with distance from the magnet bore, and even hand-held objects can be jerked free very suddenly as the holder moves closer to the magnet (Small objects, such as paper clips and hairpins, have a terminal velocity of 40 mph when pulled into a 1.5T magnet). In addition to the possibility of severely injuring someone, it is not good for the magnet to be bombarded with difficult to remove small metal 'missiles'. Remember, even when you are not scanning, the magnet is not "off". NEVER bring any metal objects into the scanner rooms.

Metal in the Body. Metallic objects in the body can also have dangerous effects when placed in a magnetic field. Ferromagnetic metal implants or fragments may twist or move, causing internal injury. Even non-ferromagnetic metal (including metal on clothing) can heat up during scanning, and cause burns or discomfort. Many of the Athinoula A. Martinos Imaging Center's subject screening criteria are aimed at avoiding these hazards. In addition, metal in or near the body (such as dental implants) can produce artifacts, which adversely effect image quality.

Gradient Magnetic Fields:

Nerve Stimulation. Another concern in MR Imaging is related, not to the strength of the static magnetic field, but to the transient application of magnetic field gradients that can induce current in conductive materials, including biologic tissue. The induced current is greater in peripheral tissue because the amplitude of the gradient is highest farther away from the magnet's isocenter. Mild skin sensations and involuntary muscle contractions, which are thought to be the result of direct neural stimulation, have been reported rarely during echo-planar imaging (EPI). This can usually be alleviated by simply repositioning the subject in the scanner.

Acoustic Noise. Another potentially hazardous effect related to gradient magnetic fields is the acoustic noise produced as current is passed through the gradient coils during image acquisition. For anatomical imaging, the noise is mostly of low frequency and has a "clunking" sound; for EPI, the noise can be of very high frequency (600-1400 Hz) and sounds like a loud "beep". Generally, the higher gradients used with higher magnetic fields and with EPI produce more intense noise. Prolonged exposure to this noise will damage the unprotected ear. Even conventional scanning procedures, which produce noise within the recommended FDA safety guidelines, have been documented to cause reversible hearing loss in patients who did not wear ear protection*. All research subjects should therefore wear hearing protection, in the form of earplugs or headphones, during scanning (both are recommended on the 3T). Also, researchers, or a parent accompanying the subject, must wear earplugs if they are in the magnet room during scanning. Earplugs must be the right size and properly inserted into the ear canal to obtain their full effect. This requires instruction and practice. It is the responsibility of the researcher to see that the subject is aptly fitted with hearing protection. Additional packing of the head with foam cushions further dampens the noise and is recommended in the 3T environment. Additional noise in the magnet environment comes from the magnet coolant pump, air handling system, and patient fan. While not dangerous, these other sources of noise can be annoying to subjects and can interfere with communication.

Radiofrequency (RF) Electromagnetic Fields:

Tissue Heating. An RF pulse (a short burst of an electromagnetic wave originating from the RF coils) is used in MRI to "excite" tissue protons by an exchange of energy. This absorption of RF energy can potentially cause heating of the tissue. Absorption of RF power by the tissue is described in terms of Specific Absorption Rate (SAR), which is expressed in Watts/kg. (In the US, the recommended SAR level for head imaging is 3.2 Watts/kg.) SAR in MRI is a function of many variables including pulse sequence and coil parameters and the weight of the region exposed. However, the actual increase in tissue temperature caused by exposure to RF radiation is dependent on the subjects' thermoregulatory system ( e.g. tissue perfusion, etc.). The risk of exposing subjects with compromised thermoregulatory function ( e.g. elderly patients and patients taking medications that affect thermoregulation, such as calcium-blockers, beta-blockers, diuretics, or vasodilators) to MR procedures that require high SARs has not been assessed.

Electrical Burns. RF fields can cause burns by producing electrical currents in conductive loops. When using equipment such as surface coils, ECG or EEG leads, the investigator must be extremely careful not to allow the wire or cable to form a conductive loop with itself or with the subject. Coupling of a transmitting coil to a receive coil may also cause severe burns.

Other Concerns:

Pregnancy. There are no known adverse effects of MRI on developing fetuses. Most early studies on pregnant animals were negative for teratogenic effects, and a recent survey found no association between working in the MR environment and a number of pregnancy outcome variables*. However, given the scarcity of data on the subject and the high susceptibility of the developing fetus to damage in general, we believe it is not worth the risk for pregnant women to participate as subjects in MR research studies. Most clinical units allow pregnant employees to enter the scan room, but not to remain in the room while the RF and gradient fields are applied during image acquisition. Pregnant researchers at the Center will regulate their own exposure to the magnets.

*For references see Shellock and Kanal, 1996, Ch. 5

Additional Information

If a subject or patient has any medical devices, you must get clearance from Steven Shannon.

For other information regarding MRI safety, please go to:

Contact Info

Steven Shannon, email:, MRI Technologist

Christina Triantafyllou, email:, MRI Physicist



Any researcher who uses the research magnet is required to set up and clean up properly. If the area is untidy when you arrive, or if equipment has not been returned to its proper position or default state, notify Steven Shannon. If you fail to notify Steven, you will be held responsible.

Set Up and Scanning

•  Only qualified persons may operate the 3T MR scanner.

•  Two members of the research team must be present during scanning, one of which should be a green badge . During tech supported hours, Steven Shannon may be the second person. Off hours each group must have two investigators, in the 3T Magnet Area (46-1158, 46-1158A, and 46-1158AA).

•  No one (including researchers and assistants) may enter the scanner room without signing a screening form.

•  Subjects that are rescanned on a different day must have a new screening form filled out.

•  Subjects must sign the appropriate consent and screening forms before they are imaged.

•  If there are any questions regarding a subject's compatibility with the magnetic field, Steven Shannon must be notified.

•  Anyone entering the scanner room must first "de-metal" outside the magnet room (empty pockets, remove jewelry, watches, wallets, beepers, hair clips, leave pens, clipboards etc.)

•  Hearing protection (in the form of earplugs or headphones, or both) must be used when scanning all subjects.

•  Double check wires on all equipment you use in the scanning room for loops that can cause serious electrical burns.

•  The scanner bed will not support subjects weighing more than 440 pounds .

•  Don't use paper clips or other small metal objects (staples, etc.) in the console room or around the scanner. They tend to land on the floor and find their way into the magnet room and into the magnet.

Clean up

•  Return all equipment to its labeled place on the shelves or in the drawers.

•  Place soiled linens in the laundry hamper in the magnet room.

•  Contaminated materials (excluding sharps) must be placed in the contaminated waste box in the magnet room.

•  All sharps are to be placed in the plastic sharps container located in the magnet room. Sharps are never to be placed in any wastebasket.

Food and Drink

•  Food or drinks are allowed in the Control Room (46-1158), but must never be on the console table or near equipment.

•  You are responsible for disposing your wrappers/waste and throw them out in the garbage can in the waiting room (1164)

•  Do not throw food wrappers of any kind in the Magnet Room Area wastebaskets.

•  Food and drinks are permitted in the waiting room (1164)

Broken Equipment

Report ALL broken equipment and equipment failures immediately to the MRI Support Team via email at MRI-all@MIT.EDU . It is understood that equipment in such constant use will occasionally break. You will not be held responsible, but we cannot fix items unless we know they are broken.

Assisting Subjects Onto The Scanner Bed

The scanner bed can be lowered, and we have a step stool in the magnet room.

The Siemens scanner beds do not detach and thus cannot be brought outside the scanner room. Do not bring wheelchairs into the scanner room. If you will be scanning a wheelchair bound subject, ask Steven Shannon for assistance.

The scanner bed will not support patients weighing more than 440 pounds .

Contact Steven Shannon for more information.


Although MR research is safe for most volunteers, for certain subjects, MRI may pose unnecessary risk. Most contraindications that would rule out a subject involve metallic foreign bodies; however, there are several other concerns of which investigators should be aware. If any question exists regarding a subject's MR compatibility contact Steven Shannon or the subject must not be scanned.

Screening and Consent Forms

In addition to screening subjects thoroughly before scheduling them for MRI, everyone must fill out and sign all appropriate Consent and Screening Forms prior to entering the magnet.

In the rare case with a person accompanying the patient in the magnet room, the visitor must be screened using the visitor screening form prior to entering the room.

Conditions that Rule Out a Subject

•  Cardiac pacemaker

•  Surgical aneurysm clips

•  Neurostimulator

•  Implanted pumps

•  Metal fragments in body / eyes

•  Pregnancy

•  Nitroglycerin patch (rule out if subject cannot remove patch; foil may heat up)

•  Certain cochlear implants *

•  Weight > 440lbs (also consider shoulder and chest size)

*Check the list of magnet compatible and incompatible products at or published book by Shellock posted in the Console Room (46-1158) and check with Steven Shannon.

Conditions that Might Rule Out a Subject

•  Ear implants (most are OK, certain cochlear implants are not*)

•  Metal rods , plates or screws in body or mouth

•  Injury to eyes involving metal (if in question do not scan subject)

•  Previous surgery (if metal left in body)

•  IUD (most are OK, except Copper-7 *)

•  Hearing aid (should be removed before scanning)

•  Dentures (should be removed before scanning)

•  History of vestibular or inner ear abnormality such as Meniere's Disease

•  Prosthetic heart valve (most are plastic now *)

•  Breast feeding (rule out if using Gadolinium)

•  Braces (causes severe frontal artifact; rule out for EPI)

•  Hair extensions (most are connected with wire, causes severe artifact)

•  Tattoos or permanent eyeliner (if ink contains metallic specks)

•  Nicotine patches (those with foil backing)

Other Screening Considerations

•  Claustrophobia

•  Physical discomfort (body size, back or neck pain, etc.)

•  Movement disorders (ticks, restless legs, etc., that may cause movement artifact)

•  Vision / Hearing problems

•  Problems using response devices

Things Not to Bring or Wear in the Scanner

•  ANYTHING in your pockets

•  Metal jewelry (face and body piercing items should be removed if possible)

•  Watches

•  Hair holders

•  Eye glasses

•  Metal on clothing (metal buttons, snaps or trimming, underwire bras, belt buckles)

•  Eye shadow (many contain metallic specks that can heat up)

For More Information

If you have any doubts whether a subject is magnet compatible, do not scan. Contact Steven Shannon.

For additional MR safety information visit




Steven Shannon will hold training sessions every few weeks at the Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research. Notifications of these training sessions will be announced by Steven via email to MRI-all@MIT.EDU.

Please note that if you intend on imaging at MGH you must attend the safety training at the Martinos Center for Biomedical Imaging at MGH Charlestown.

Our training system consists of three levels,

1) White = Safety

2) Yellow = In Training (for all areas)

3a) Green = Certified Scanner for human scanning on the 3T Tim Trio

3b) Dark Blue = Certified Scanner for Animal scanning on the 3T Tim Trio.

The descriptions of each role are below. We have developed this system so we can better keep track of what level each person is at in his or her training, and ensure that each person has received the proper training to work around the MRI scanner.

***If you do not have a badge, you should not be in the 3T area (46-1158, 46-1158A, or 46-1158AA).***

Badges usually take up to 2-3 business days to make. Steven Shannon will send an email notifying you when your badge is ready. Badges may be picked up in room 46-1171.

The MRI team (Christina Triantafyllou, Steven Shannon, and/or Sheeba Arnold) reserves the right to refuse anyone permission to operate the 3T magnet.

I. Description of Training Levels

1) White = Safety:

A person who can be present during the scan and is available to get help or to assist in the case of an emergency. This person does NOT assist with the set up of the subject or run the scanner or any of the equipment (this includes stimulus equipment). With this white SAFETY badge, the person is allowed to sit in the scanning area for emergency purposes ONLY under the supervision of a person at the Certified Level Status.

Training requirements to obtain a white SAFETY badge include:

Step 1: Watch the safety video (~20 minutes)

Step 2: Take and pass the Safety Training Test (passing score is an 8 our of 10 (~5-10 minutes)

Step 3: Attend the 1st half of Steven's Lecture (the safety portion) (~30 minutes). Altogether this training session takes approximately 1 hour.

2) Yellow = In Training:

This is a person who is present during the scan session and is in training to learn the finer details of running the scanner. This badge allows the person to assist with the setup of the subject in the magnet room, setup and run the stimulus and scanner equipment, and assist in an emergency under the supervision of a person at the Certified Level status (See Manual for further details).

Training requirements to obtain a yellow IN TRAINING badge include:

Step 1: Watch the safety video (~20 minutes)

Step 2: Take and pass the Safety Training Test (passing score is an 8 our of 10 (~5-10 minutes)

Step 3: Attend the 1st half of Steven's Lecture (the safety portion) (~30 minutes).

Step 4: Attend the scanner/console training portion at the Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research (~40 minutes).

3a) Green = Certified Scanner for Human scanning on the 3T Tim Trio

3b) Blue = Certified Scanner for Animal scanning on the 3T Tim Trio

This person has completed steps 1-4 of the initial training and typically participates in at least 5-6 additional training scan sessions with fellow lab members, who are already certified to scan, until the person in training becomes proficient in scanning and MRI safety (see list on last page of packet for checklist of items each person should be able to do for either 3a or 3b above). For someone who is training for the 3T scanner and feels like he/she is proficient with everything on the checklist: email Steven Shannon to set up an assessment appointment. He will observe you during a scan session with a real subject to determine your qualification to become a "Certified Scanner".

II.Training Program Contents

Magnet Safety

•  Safety video

•  Emergency procedures

•  Stop scan buttons

•  Calling for help ( MIT Emergency 100 )

•  Getting the subject out of the magnet

•  Adverse event reporting

•  Magnet Area orientation

•  Rules for equipment use

•  Reporting equipment problems

•  Where to find coils, linens, supplies

•  How to use coils, linens, supplies

•  Subject preparation

•  Informed consent

•  MR screening

•  Demetaling

•  Hearing protection

•  Positioning in magnet and landmarking

•  Squeeze ball

Using the Testing Equipment

•  Computers

•  Audio

•  Video

•  Response box

•  Physiological monitoring

Operating the Magnet

•  Login/Logout

•  Scanning

•  Archiving and retrieving data

•  Discovery of a potential physical abnormality


•  Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research Policies and Procedures for Human Subjects

•  Safety Rules for the Magnet Environment

•  Safety Hazards

•  MR Compatibility Screening

III. Evaluation and Certification Procedure

•  View Safety Video

•  Complete Training

•  Scan a subject or phantom with a MRI Support person present ("qualifying exam")


IV. Center Record Keeping

The Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research will keep records of all investigators certified to operate the 3T Tim Trio including:

•  date safety video viewed

•  date training course part 1 (safety portion) completed at Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research, trainer

•  date training course part 2 (scanner/console portion) completed at Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research, trainer

•  date of qualifying scan session


Tips for scanning on the Siemens Tim Trio Scanner


There are four task cards along the right hand side of the screen: EXAM, VIEWING, FILMING, and 3D (Fig. 1, red arrows).

  • EXAM is the interface that allows us to acquire data.
  • VIEWING is where you can look at images that have been previously collected.
  • FILMING is where you can prepare images to be printed (please see the “printing the slice prescription” section below).
  • 3D allows you to view 3D datasets (Structural MPRAGE) in all three orientations.

Figure 1: Registration

You want to select the EXAM card to start your study.

  • Next, in the Patient pull down menu (top left hand corner) select Registration, alternative press the key on the keyboard (right hand corner) that has a small man and a keyboard on it.  Pressing this will also bring up the registration. A form will appear and you need to fill in all the boxes that have bold writing (Fig. 1, black arrows).  You will not have an option to click EXAM until all these are filled out. Remember never use patient identifiers as this is a violation of the Health Insurance Portability and Accountability Act (HIPAA)
  • A suggested name for your subjects is XXX_YYY_ZZZ, where X is the first 3 letters in the Principal Investigator’s Name, Y is a paradigm name, and Z is the subject number.  This should be copied and pasted into the Patient ID field.
  • Date of birth should be listed with the date and month as 1, and the actual subjects year of birth (example: 1/1/1980)
  • Do not forget to select the sex, this is often missed
  • Enter the subjects weight in pounds
  • For the study, press the arrow and click on INVESTIGATORS, then select your name or the name of the PI.
  • For patient position press the arrow and select the first option. Head First - Supine.
  • Although they are not mandatory for scanning you need to enter the PIs name in the physician box and your name or initials in the operator’s

When the information is entered press the exam button. Another window will appear asking you to verify that your information is correct.  If it is, press confirm.


On the lower right half of the screen all of the sequences within the protocol will appear. To actually scan you must move them over to the lower left by dragging them over (Fig. 2, arrow), or highlighting the sequences you want and click the (<<) button.

Figure 2 : Start Up

  1. The first sequence is always a localizer , followed by the Auto Align (AA) localizer ( AA Scout ). Highlight these sequences and then click the double arrow (<<) to move it over to the left. You can see that these localizers do not have the small man icon beside them, as the others below it have. Once they are moved they will automatically run. All of the parameters have been pre-programmed. When scanning is complete a sagittal, axial, and coronal image will appear in the 3 upper segment of the screen. For the AAScout, wait until the images are fully reconstructed before you run the next sequence.
  1. Please note: If you are using AAScout (Autoalign), the sequence should run with the Bodycoil, otherwise it may fail. Also, you should ensure that the AutoCoil selection is OFF (Topbar-> Queue->Auto Coil Select) so that Autoalign does not start automatically for example with the 32Ch coil. Autoalign allows the slice placement of subsequent scans to automatically align (default is parallel to the AC/PC Line). When Autoalign is acquired successfully an icon with a yellow line appears (Fig. 3, yellow arrow), if it was not successful it appears with a red line. When using the AA Scout, once you move the next sequence (for example, Structural MPRAGE) to the left hand side and open it, (by either double clicking on it, hitting the open button, or right clicking it and selecting open), in most cases the sequence will open properly positioned to the brain (i.e. tilts slice box to compensate for the subjects positioning). You should always check to verify slice position is correct. However, if you do not use the Autoalign, the user is responsible for positioning the slice prescription for the rest of the protocol.

Figure 3 : Opened Protocol – Routine Tab

  1. The structural scan (T1 MPRAGE) should be brought to the left panel and opened as described in point 2. Once opened the sequence parameters will be in the lower right side panel. The parameters are displayed on many tabs but always open on the Routine Card (Fig. 3, black arrow) showing the selected coil elements (Fig. 3, red arrow). If it does not indicate the proper coil elements something is wrong (i.e. protocol uses different coils, unplugged coil, or Auto Coil Select is on). To change coil elements you need to go to the system tab and select the appropriate coil elements (Fig. 4, black arrows). The sequence will not run until you position your slices/volume. The yellow boxes over the localizers represent the area to be scanned. Anatomy cut off (such as the nose) can wrap and end up in the occipital lobe. Make sure the slice prescription is correct. If needed, you can move or tilt the slices (volume). Left clicking the center dot allows you to move the volume. If you need to rotate the volume move the cursor down over the centerline until you see a double arrow, hold the left mouse button down and rotate as needed. Grabbing any of the sides can change the FOV or slice thickness. Tell the subject that the sequence is going to begin and click “Apply”.

Figure 4 : Coil Selection - System Tab

  1. Manual adjustment of the shim is also possible. The icon of a head with pink lines (Fig. 4, red arrow) will bring up the shimming toolbox amongst other tools. Click the icon and select the second from the right on the bottom row. This will activate a green box you may tighten the shim around the brain. The center circle centers the box. The diamonds on the side make it smaller or larger and if you put the cursor over one of the sides a circular arrow appears and you can now angle the box. When every thing is set hit “Apply” and the scan will start. Please note that this will setup the shimming option in your protocols to manual instead of automatic adjustment.

Figure 5 : MPRAGE

  1. When the first structural scan has completed reconstruction, a head profile icon will appear (Fig. 5, arrows). Drag the icon with the left mouse into one of the three window segments (Fig. 5, far left window). If more than one series is present under the head profile icon, click on the icon and drag only one series at the time. Please note that the center slice of this series will appear in the window. Use the dog-ears in the right corner to go forward and back in the image series until you find the best slice. Also, go through the entire series to check for motion or possible abnormalities. If you see an abnormality call Steve, if not continue.

In cases that AA Scout was used, all sequences can be brought over to the left hand side of the page, opened by double clicking on the sequence or hitting open (slices are automatically centered) then hitting “Apply”. Please note that on occasion AutoAlign may fail, therefore make sure the slices are orientated as required. If manually setting up your slice prescriptions follow below.

  1. At this point it is recommended that you run a test EPI functional run with 2 measurements (time points) to ensure the slice positioning and quality are good. You can use your regular fMRI sequence manually changing the measurements located on the BOLD Card (Fig. 6, arrow). This should be done before you run any other optional scans such as the field map or T1w EPI scan.

Figure 6 : BOLD Tab

  1. Bring over the T1w EPI sequence (if required). Copy the exact slice prescription as the functional scan. To achieve this, open the T1w EPI sequence and with the right mouse highlight the 2 measurement functional run with the proper slice positioning, then select copy parameters from the menu. From the list of parameters you want the second option, slices & sat parameters. Please follow the instructions in step 3 if slice volume needs to be adjusted. Now the T1w EPI slices are in the same location as the 2 measurement functional run (step 6). Hit “Apply” when positioned properly.
  1. Bring over the field map and open it. With the right mouse highlight the 2 measurement functional run with the proper slice positioning and select copy parameters from the menu. From the list of parameters you want the second option, slices & sat parameters. Now the field map is in the same location as the 2 measurement functional run (step 6) and you can hit “Apply”.
  1. Bring over the functional EPI and open it. Copy the slice prescription of the 2 measurement functional run just as you did for the T1w EPI and field map (step 6). The acquisition time of the scan will be indicated at the upper left corner of the sequence. Remember that the time reflects the 4 dummies scans so; deduct 4x the TR from the time of the scan to calculate the delay from the start of your paradigm. Click “Apply”.

Figure 7 : Inline Display

  1. Because you have the wait for user to start on (icon of man holding a flag) a pop up window will appear, click continue when you have everything ready to go. If you want more runs with the same slice prescription but a different # of measurements, highlight the functionals with the right mouse, append, open, and make the changes as described in step 6 and click “Apply”.
  1. Make sure to open the Inline Display (Fig. 7, arrows). Inline Display shows your functional images immediately after the images are reconstructed. This allows you to monitor if your subject is moving, or if there are unwanted artifacts.

Printing the Slice Prescription:

•  Make the sagittal with the slice prescription the active window by clicking on it. A blue box will appear around it.

•  Hit the button in the lower right hand corner of the keyboard that look like a sheet of film. This will send the active image to the filming page.

•  Go to the filming page, a tab on the right of the screen. The image will be in the upper left hand corner of the page. Click the edge of the film border, (multiple blue boxes will appear) then click the layout tab on the lower right and choose the single image layout. It should now be large.

•  Go to the camera tab and make sure that the setting is for the laser printer and the normal setting (not inverted).

•  Click the icon that looks like a printer with a sheet of film coming out of it, this is the printer. The image comes out of the paper printer.

Making a CD & Sending Data to the DICOM Server:

•  Label a CD and put it in the top draw of the burner. Make sure you do not hit the round silver button. This shuts off the computer, it does not open the cd-rom. There is a small black button below the drawer that opens it.

•  Highlight your study from the browser. The browser can be activated through the patient pull down menu or by hitting the button in the lower right hand corner that has a folder tree file on it. Highlight your subject up to but not including any of the series. Go to transfer pull down menu select export to CD-R.

•  Next a window appears asking you to label the CD. There is also a check box that you can click if you want the viewing options from the system on the CD. A CD icon (a CD with a red ball on it) will appear on the bottom of the screen. When the icon is gone, the burning is complete.

•  If that data does not fit on one CD a pop up message will appear when the first CD is finished. You should click eject, and insert a blank CD. You then must click retry to continue burning your exam (retry burns the second disk, it does not retry the first CD!)

•  Go back to the transfer menu, select "sent to" and choose Sigma. Your study will now go to the server. Go back to the transfer menu and select local job status to make sure the cd transfer is working or select network job status to make sure the DICOM transfer is working.


All warning and errors present as pop up boxes and/or listed in the MR Scanner and Acquisition or Background icons (Fig 1a) located at the bottom of the screen.

Figure 1a: MR Scanner and Acquisition or Background

Figure 1b: Warning

Figure 1c: Error

In the event of a warning (Fig. 1b) or error (Fig. 1c) there would be a yellow or red slash through one of these icons.  To view what the error/warning is click on the icon.  A pop up box will have the message.  If you choose okay it will clear the messages.  If you press the close button it will keep the message.  Write down this message in the error logbook provided or do a screenshot and send the message to

Please note the warning or error and check the status of that component via the System Manager.  To access the System Manager go to System --> Control via the top pull down menu (Fig. 2). 


Figure 2: System Manager

  • Go to the system pull down menu from the top of the scanner page and select control. There are 4 tabs on the top. You need to look at the image recon and MR scanner options. If all is well they will have green checks and xs. If any of them is red select the reboot option and wait about 3 minutes.
  • If rebooting does not work, take the table all the way out and unplug any coils you are using. Now go to the system pull down menu, select system end and then check the restart system box. This should take about 5 minutes for the system to go down then restart.
  • If system restart does not work, bring the system down. At the scanner locate system on the pull down menu and then select end. Select shut down all and then click ok. When the message appears that it is now safe to turn off your system hit the blue off button on the Siemens box located to the right of the console.
  • Wait about 2 minutes and press the system on button (the key on then box must be in the unlocked position). A message stating contact you service rep, finding occurred will appear; just click ok. You do not need to write this in the book or contact Steve. Gunjan (Siemens service rep) checks the logs regularly. If all goes well, you will hear 3 beeps in about 20 minutes.

Figure 3: Host tab

The Host tab (Fig. 3) allows you to:

  • Restart an individual task cards (Exam, Viewer, Filming, 3D, etc...)
    • Click the appropriate task card and press restart application. 
      (Time to complete ~ 30 seconds)
  • Restart the Siemens Syngo program
    • Press the "Restart syngo MR" .
      (Time to complete ~ 5 minutes)
  • Reboot the Host computer (this also reboots MR Scanner)
    • Press the "Reboot" button .
      (Time to complete ~ 7 minutes)
  • Restart the entire system
    • Press "shutdown all" to shutdown the entire system.  Once the screen states it is safe to shutdown you will need to press the blue “system off” button on the Siemens Alarm box (Fig. 4). Wait a couple of minutes and then press the blue “system on” button.  An alternate method to restart the entire system is to select System --> End Session via the top pull down menu (Fig. 5) and press restart system (Fig. 6).
      (Time to complete ~ 22 minutes)

Figure 4: Siemens Alarm Box

Figure 5: System End Session

Figure 6: Restart System

The Image Reconstruction System tab (Fig. 7) allows you to:

  • Reboot the Image Reconstruction System
    • Press the “Reboot” button 
      (Time to complete ~ 3 minutes)

Figure 7: Image Reconstruction System tab

The MR Scanner tab (Fig. 8) allows you to:

  • Reboot the operating system of the MR scanner
    • Press the “Reboot” button 
      (Time to complete ~ 3 minutes)
  • Switch the Scanner to Standby (This basically shuts everything but the console) 
    • Press the “Stand By ” button 
      (Time to complete ~ 1 minutes)
  • Switch the Scanner out of Stand By Mode
    • Press the "System On" button

Figure 8: MR Scanner tab



If the table freezes here are 2 quick solutions:

•  Hit the red button on the scanner and then move the table in/out buttons back and forth until you hear a "click". Then press the table forward once and release. Watch for an arrow to appear at the head and feet of the icon on the display. The table is now reset.


•  You can go out to the console room and hit the host standby button on the white Siemens box. Wait a minute and hit the on button. Wait for 3 beeps and the table will be reset.






Martinos Imaging Center - 43 Vassar Street. 46-1171, Cambridge, MA 02139 - Tel: (617) 324-2702, Fax: (617) 324-2701, Email: mri-team at mit dot edu