Starting an MRI Study

GE MRISo you want to start a MRI study? Well, there are several things that need to be addressed. This document will help make sure that you have prepared yourselves for your first scan session.

Your research question and experimental design are very important aspects to collecting useful data.  We have trained staff here in the lab than can help you make decisions regarding the design of your experiment. Please contact Michael Anderle, the Lab Manger, to help you seek these folks out.

After you have worked out a design for your study, it is time to start thinking about the nuts and bolts of getting things up and working.

1. Human Subjects Committee Approval

HSC approval is critical to your study's existence. The Human Subjects Committee must approve your research protocol before any subjects can be run. They have a website that outlines this process and provides you with all the necessary forms to initiate the approval process. All investigators must also complete the online human subjects training.

HSC approval can be a lengthy process, so submit your protocol as soon as it is finalized. As a recommendation, we suggest you include the ability to run 2-3 single session pilots as well as the subjects you need. With this, you can do testing before the first subject. Regarding consent forms, note that all physiological measures that need to be collected must be included in the form (cardiac, respiration, SCR, eye tracking, etc.). Also, your consent form you will want to include information about "adventitious findings."

Once you have received HSC approval for your protocol it is time to fill out the needed forms.

Form #1 The MRI Time Request Form. This form will ask for various information (i.e., funding source, HSC approval number, number of subjects, etc.).

Form #2 The Acquisition Strategy Request Form. This form will ask for information pertaining to your hypothesis, statistical analysis, and paradigm design (PDF).

Form #3 The Network Storage Form. This form is for users who will be using lab disk space to analyze data. If you are going to analyze your data at a different location you do not need to fill out this form.

After you have filled out the forms email Michael a copy of your approved Protocol and stamped Consent Form(s). Once Michael has all the needed documents a MRUsers committee meeting will be held.

The MRUsers committee will sit down and review the time request, the acquisition strategy form, the IRB approved protocol, and consent. They will make sure the lab can supply you with any special requests you have and then check what times you have suggested for scanner time with our own scan calendar to see what is available. To see MRI availability, you can contact Michael Anderle to receive instructions on how to access our online calendar.

2. Safety Training

The next step is safety training. The MRI environment is one that has the potential to be extremely dangerous to you, your staff, and to your subjects. The highest safety precautions need to be taken to ensure that no accident will happen. Everyone in your research group who will be present during your scans must watch the safety video and be safety screened by someone who is qualified to do so. No data will be collected until everyone involved with your scans has seen the video tape and been safety screened. A good point to consider is that it is better to have fewer people involved with scans as possible - fewer people, fewer possible accidents.

To see the video and be safety screened, please contact Michael Anderle at 265-6250. More information on MR safety.

3. Equipment Set-Up

Once you have seen the MRI safety video and have been screened you can now have access to the stimulus equipment and magnet room. For visual stimulus presentation, we have the Avotec Silent Vision System, and a video back-projection system. Integrated into the Avotec Silent Vision System is our iView eye-tracking system. For audio stimulus presentation, we have the Avotec Audio System and Resonance Technology Audio. There are three intercom systems that can be used to communicate with the subject. One is integrated into the scanner, the other two are part of the Avotec Audio System and Resonance Technology Audio. For stimulus delivery, we have a PC equipped with XP running E-Prime, Presentation and DMDX. The display to the goggles can be either monoscopic or stereoscopic. To record subject responses while they are in the magnet we have a four button inline button box, a four button bi-manual button box, and a USB joystick, all of which are integrated with the stimulus PC. To ensure data quality, we have several ways to help the subject hold their head still.

Lastly, as well as collecting MRI data, you can also acquire ancillary measures via the Biopac system. These measures include, ECG, SPO2, end tidal CO2, temperature, EMG, EDA, and respiration. Also available are pupilometry and eye tracking which are integrated into the Avotec goggle system. Recall that all of these measures must be integrated into your IRB protocol. If you have any questions about these measures, please contact Michael Anderle.

The best way to figure out what systems you are going to use is to sit down and learn the capabilities of each. We have trained staff here that can help you make these decisions. The best thing that you can do is not rush into scanning. Take some time to carefully plan out what scan equipment will be used and then test it many, many times with your paradigm. This will ensure that when it comes time to run a real subject, everything works correctly. To set up time to go over the equipment and learn the rules of the MRI control/scanning room, please contact Michael Anderle.


4. Protocol: Scans

Once you have all of your equipment set up, it is time to think about the scans you want to collect. The protocol is the list of scans that will be run during your scan session. In general, the technician needs to know what anatomicals to collect, how many fMRI scans you want to collect, and how long those scans are.

The parameters of these scans vary from study to study. What parameters you use will be determined by what area of the brain you are looking at. If you have questions about scans and/or parameters, we have trained people here in the lab who can help you.

5. Subjects

Lastly, you need to know how to go about preparing your subjects. On first contact, it is important that you do a metal screen. This is the metal screening form that we use. You will be taught how to use this form when you, yourself, get screened. If a question arises as to whether or not the subject screened is MR compatible, contact Michael Anderle for more information. Often times if something does come up on a subject's screening form you will be asked to get a Dr's note. What we need is a signature from a trained medical professional that states that your subject is safe to go into the 3.0T MRI scanner. If we can not get this form signed, we can not scan your subject. Please see the doctor's form HERE.

Depending on your subject population, you may want to "simulate" your subjects before they come to their scan. If your subjects are younger or have a condition that would prevent them from relaxing in the scanner, you may want to acclimate them to the unique environment of the MRI before the scan. To do this, the lab uses a simulator room, with a mock MRI scanner, fiber optic goggle system, and auditory system with two control computers. This room helps you introduce your subjects to the identical experimental procedures that they will experience in the actual scanner. This helps ensure subject comfort and good data quality. If you choose to run simulations on subjects, it is best to schedule the "sim session" approximately a week before the scan. To see the simulator room availability, you can contact contact Michael Anderle to receive instructions on how to access our online calendar.

On the day of the sim session, you should again do a metal screening form to make sure nothing has changed since your first contact. If it has, having the simulator session one week prior to the scan date gives you time to check with the appropriate people to make sure your subject will be safe. At the end of your simulation session we have made an information sheet to give to your subjects. If you are not going to run a simulation, the information on this sheet should be read to the subject via phone.

6. Day of Scan

The day you have been waiting for! On this day you will want to arrive approximately 30 minutes to 1 hour before your scan. This gives you time to prep the magnet room, test the equipment with your paradigm, and give any questionnaires to the subject before the scan. Quite often we run scans back to back throughout the day.  With this, we need people to be considerate of both the incoming and outgoing scans.  A good practice is to quietly check to make sure the prior scan is running on time.  This way you can make adjustments if need be.

Many investigators use a Run Log that has a detailed account of what needs to be checked with the equipment to make sure all works and runs smoothly. Do not assume that because everything worked the week prior that the setup has not changed. Many groups use our facilities and have particular setups that modify the equipment. You need to test everything (stimulus presentation, button box response, eye-tracking calibration) to make sure your study will work.

We have a subject prep room right outside the magnet room T170. You have access to this room for one hour before your scan. At this time, you may give any last questionnaires needed, have the subject fill out the consent form, do one last metal screening, and de-metal the subject. After the subject has been prepped, you will want to bring the completed screening form and consent form to the technician. The technician will then take that information and enter it into the scanner. The technician can not scan until he or she has both an up-to-date screening form and a signed consent form with an HSC stamp of approval. After the technician is ready, he will have you go get the subject and do one last verbal metal screen. At that point, the subject can then - and only then - enter the magnet room. If you need to administer more questionnaires after your scan you can get a testing room in the Waisman Center. Please remember that the next group will be in the subject prep room by the time your scan is done.

7. Data

After data has been collected the dicom images and physiologic data will be immediately transferred off the scanner and onto our lab /study drive. The technician will make a backup of the anatomicals onto DVD. It is very important that you check the study drive after your scan to make sure all files have transferred successfully. The dicom images will be left on the scanner for a short duration after the scan, but will be deleted before a weeks time. Note, it is the investigators responsibility to transfer the eyetracking data to the study drive.

8. Pilot Scan Policy

It is the policy of the Waisman Laboratory for Brain Imaging and Behavior to provide free of charge, a limited number of MRI pilot scans for research projects. Most projects are able to sufficiently check their parameters, data quality and protocol logistics within three, two-hour scanning sessions. Extenuating circumstances leading to additional piloting time will be evaluated on a case-by-case basis. This policy is not intended to cover entire pilot projects for specific research programs, unless the goal of the project is to develop a new pulse sequence, test new equipment in the MRI scanner room, or otherwise contribute to the development of new methodological capabilities for the facility. Such pilot projects require approval of the Director.

This policy does not extend to PET or microPET scans.