Athinoula A. Martinos Imaging Center MRI Safety and Operations Training Manual
1. EMERGENCY INFORMATION FOR THE MR AREA
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)
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, 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 http://web.mit.edu/committees/couhes/forms.shtml . 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:
http://www.MRIsafety.com.
2. HAZARDS OF THE MR ENVIRONMENT
"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 a few decades 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
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 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 - 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. 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.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 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.
Additional Information
If a subject or patient has any medical devices, you must get clearance from Steve Shannon.
For other information regarding MRI safety, please go to: MRIsafety.com.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 3. MR SUITE SAFETY RULES
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 researchers may operate the 3T MR scanner.
• Two members of the research team must be present during scanning, one of which must be a green
badge. During tech supported hours, Steven Shannon may be the second person. Off hours each group
must have two researchers in the 3T Magnet Area (46-1158, 46-1158A).
• 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 otherwise do not have the subject enter the scanner area.
• Anyone entering the scanner room must first "de-metal" outside the magnet room (empty pockets,
remove jewelry, watches, wallets, phones, hair clips, 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.
• 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 or linen closet.
• 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 (46-1164)
• Do not throw food wrappers of any kind in the Magnet Room Area wastebaskets.
Broken Equipment
Report ALL broken equipment and equipment failures immediately to the MRI Support Team via email at
MRI-Team@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.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 4. SCREENING SUBJECTS FOR MRI COMPATIBILITY
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 researchers 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 area.
In the rare case with a person accompanying the patient in the magnet room, the visitor must be screened
prior to entering the room jus like you would do with your subject.
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 www.MRIsafety.com and contact with
Steven Shannon.
Conditions that Might Rule Out a Subject
• Ear implants
• 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 (some are safe)
• Hearing aids (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 *)
• 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)
• 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 doubt whether a subject is magnet compatible, do not scan. Contact Steven Shannon.
For additional MR safety information visit http://www.MRIsafety.com
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 5. MR SYSTEM OPERATION AND SAFETY TRAINING
EVERYONE INVOLVED IN RUNNING AN EXPERIMENT ON OR AROUND THE RESEARCH
MAGNET IS REQUIRED TO ATTEND A MRI SAFETY CLASS.
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.
Our training system consists of three levels,
1) White = Safety, this person is not authorized to enter the magnet room.
2) Yellow = In Training (for all areas)
3) Green = Certified Scanner for human 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 461158AA).***
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 must be picked up in room 46-1171.
The MRI team (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: Attend the 1st half of Steven's Lecture (the safety portion)
Step 2: Take and pass the Safety Training Test (passing score is an 8 our of 10 (~5-10 minutes)
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.
Training requirements to obtain a yellow IN TRAINING badge include:
Step 1: Attend the 1st half of Steven's Lecture (the safety portion)
Step 2: Take and pass the Safety Training Test (passing score is an 8 our of 10 (~5-10 minutes)
Step 3: Attend the scanner/console training portion at the Athinoula A. Martinos Imaging Center at the
McGovern Institute for Brain Research.
3a) Green = Certified Scanner for Human scanning on the 3T Tim Trio
This person has completed steps 1-3 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. 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".
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research II.Training Program Contents
Magnet Safety
• 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
III. Evaluation and Certification Procedure
• 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 training course part 1 (safety portion) completed at Athinoula A. Martinos Imaging Center at the
McGovern Institute for Brain Research.
• Date training course part 2 (scanner/console portion) completed at Athinoula A. Martinos Imaging Center
at the McGovern Institute for Brain Research.
• Date of qualifying scan session
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 6. RUNNING PROTOCOLS
Tips for scanning on the Siemens Tim Trio Scanner. This includes
• Registration
• Scanning
• Printing a slice prescription
• Making a CD and sending data to the DICOM Server
• Troubleshooting
• Resetting the scanner table
Registration:
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
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research •
•
•
•
•
•
•
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.
Scanning:
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.
1.
2.
Figure 2 : Start Up
The first sequence is always a localizer, followed by the Auto Align (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.
Please note: If you are using AAScout, the sequence should run with the Body coil, 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
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 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.
3.
Figure 3 : Opened Protocol – Routine Tab
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 opens 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”.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 4.
Figure 4 : Coil Selection - System Tab
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 everything 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.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research 5.
6.
7.
8.
9.
Figure 5 : MPRAGE
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.
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
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.
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”.
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”.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research Figure 7 : Inline Display
10. 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”.
11. 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 dotted 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 lower drawer of the Host computer. 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.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research • 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 CD 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.
TROUBLESHOOTING:
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 mriteam@mit.edu
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).
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•
•
•
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. If any of them are 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. If all goes well, you will hear 3 beeps
in about 20 minutes.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research Figure 3: Host tab
The Host tab (Fig. 3) allows you to:
• Restart an individual task cards (Exam, Viewer, Filming, 3D, etc...)
o Click the appropriate task card and press restart application.
(Time to complete ~ 30 seconds)
• Restart the Siemens Syngo program
o Press the "Restart syngo MR" .
(Time to complete ~ 5 minutes)
• Reboot the Host computer (this also reboots MR Scanner)
o Press the "Reboot" button .
(Time to complete ~ 7 minutes)
• Restart the entire system
o 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)
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research Figure 4: Siemens Alarm Box
Figure 5: System End Session
Figure 6: Restart System
The Image Reconstruction System tab (Fig. 7) allows you to:
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research •
Reboot the Image Reconstruction System
o 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
o Press the “Reboot” button
(Time to complete ~ 3 minutes)
• Switch the Scanner to Standby (This basically shuts everything but the console)
o Press the “Stand By ” button
(Time to complete ~ 1 minutes)
• Switch the Scanner out of Stand By Mode
o Press the "System On" button
Figure 8: MR Scanner tab
RESETTING THE TABLE:
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.
Or
• 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.
2012, Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research