Starting an MRI Study
So you want to start a MRI study? Well, there are several things that need to be addressed. This doucment 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 at the lab than can help you make decisions regarding the design of your experiment. You will need to complete the Acquisition Strategy Request Form online prior to arranging for scan time (you can download a PDF first, if you like).
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 would suggest that when you write up your protocol that, as well as describing everything your experiment includes, your consent form gives you the ability to run 2-3 single session pilots as well as all of the subjects that you want to include. Note: All physiological measures that you would like to collect must be in your consent form (cardiac, respiration, SCR, eye tracking, etc.).
Also, in writing your consent form you will want to include this information about "possible findings."
Once you have received HSC approval for your protocol it is now time to fill out the "MRI Time Request." This form will ask for various information (i.e., funding source, HSC approval number, number of subjects, etc.). You are to fill out the entire form. Once this form has been submitted it goes to Donna Cole, our Lab Manager, to organize a MRUsers committee meeting.
The MRUsers committee will sit down and review the time request and the standard neuroimaging protocol submitted earlier. We 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 that you need to address is safety training. The MRI environment is one that has the potential to be extremely dangerous to you 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 will need to watch the safety video and be safety screened by someone who is qualified to do so. No scans 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 Donna Cole @ 265.8107. More information on MR safety.
3. Equipment Set-Up
Once you have seen the MRI safety video and have been screened you now can have access to the stimulus equipment. For visual stimulus presentation, we have the Avotec Silent Vision System, Resonance Technology Goggles, 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. To record subject responses while they are in the magnet we have a four button inline button box, a two button bimanual 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 the brain data you can also acquire ancillary measures such as heart rate, respiration, pupilometry, eye tracking and skin conductance data. 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 very important 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 a time to go over the equipment and learn the rules of the MRI control/scanning room, please contact Michael Anderle.
4. MR Protocol
Once you have all of your equipment set up and your paradigm elicits the desired response, it is time to start thinking about your MR protocol. An MR protocol is a sheet that will be given to the scan technician on the day of the scan. This will give the technician instructions as to what parameters to use when scanning your subjects. In general, the technician needs to know what anatomicals you want to collect, and how many fMRI scans you want to collect. Most of this should have been covered when you completed the Standard NeuroImaging Protocol Description.
The detailed side of this will include things such as TR and TE, the acquisition orientation, flip angle, whole/partial brain coverage, slice/gap, fov, number of slices, and number of boldreps in the fMRI scan. If you have questions about any of these parameters, we have trained people here in the lab who can help you. Many of the parameters in the MR protocol will be determined by which areas of the brain that you wish to look at. To have an example protocol sent to you, or if you have questions about what parameters you should use, please contact Michael Anderle.
5. Subjects
Lastly, you need to know how to go about preparing you subjects. Upon first contact, it is imperative that you do a metal screen. This is the metal screening form that we use here at the Brain Imaging Laboratory.
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. The reason we do the metal screening on the first contact is you want to be able to find out right away if the person in question will be MR compatible and not waste any other time if, for some reason, they are not.
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, physiologic data, and p-files will be immediately transferred off of the scanner and on to our study drive (Y:) in the lab. The technician will make a backup of the anatomicals on optical disk for archive. 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 the week is up. Note, it is the investigators responsibility to transfer both eyetracking data and SCR data to the study drive.
Lastly, before you start processing your data, you will want to make a backup of both dicom images, physiologic data, and p-files. If you will be processing your data elsewhere there are two routes we can take:
1. we can put both dicom images, phys data, and p-files on an anonymous ftp server, or
2. we can burn data to CD rom.