🧠fMRI Protocol

Pre-Scan Procedures

Before Participant Arrives

You need to arrive at least 15 minutes prior to their scheduled start time on the Google Calendar.

1. Open the ONR fMRI SharePoint Page

   • Open the Subject Database and Scan Log in separate tabs

2. Open the Lab Email to see if the participant has messaged us and is still coming

3. Print their paperwork. If you scroll down on the ONR fMRI SharePoint Page there is a section Forms to Print with their MRI forms. Find their name on the Google Calendar

   • Consent Form - Last page only (pg 8)

     • If it is not signed by a researcher, sign it

   • MRI Screening Form - Both pages double sided

These next items can also be completed after the participant arrives and while they are doing the practice tasks

1. Add them to the Scan Log

   • In CC column plug in the next Counterbalance_Condition number (1 through 6) and it will give you the Task Order.

2. On the Subject Database column CABI Session put in today's date

3. Fill out the MRI Requisition Form

   • Be sure to fill out the URSI (M#) and the Study Subject ID (18#)

   • Make a note on the top for the Scan Order (e.g. 1b, r, 3b)

Participant Arrives

1. The doorbell will ring when they are at the side door. Go and get them. Bring them to the practice room

What if they participant does not show up on time?

• Occasionally, they will come to the front door and be waiting in the lobby. If it is a few minutes past their start time you might want to go check the front

• If they are 5 minutes late, give them a call to verify they are on their way or they need to cancel

1. Give them an overview of what will be happening today

   • About 15 minutes in here to practice what they will be doing in the scanner

   • They will be in the scanner for up to 1 hour 20 minutes

   • Ask them if they have been in an MRI Scanner before

     • If yes, ask them if it was for a brain scan / go over with them what the scanner environment is like

     • Tell them:

       • Laying down on their back and will go fully into the MRI bore which is a small enclosed tunnel.

       • Because it is a brain scan there will be a head coil over their face

     • Scanner is noisy

   • Make it clear to them that if at any point they are disoriented or too uncomfortable that they can stop the scan at any time

   • Also let them know that most people find it very relaxing in there but they need to stay alert during the task scans

2. Have them verify the first page of their MRI Screening Form and have them initial and date at the bottom of the page

Baseline and Practice Tasks

1. Start them on the baseline task (always do the baseline first)

   • Setup and calibrate the eye tracker. Same as we do in the JS Coon building

     • Tell them to sit in a position they can maintain cofortably for 5 - 10 minutes

     • Adjust the monitor so that it is 60 - 70cm away

   • Let them know when it goes to a red screen to come get you. Let them start by pressing the spacebar (don't interrupt the baseline measure) - close the door

2. Start them on the next task based on their counterbalance condition - find it in the Scan Log

   • They can read the instructions themselves, just check to make sure they respond on every letter

3. Start them on the last practice task

Setup MRI Environment

Head to MRI Suite

When they are done with the practice tasks you can bring them over to the scanner room

1. Grab the Consent, MRI Screening, and Requisition Forms

2. As you walk them over the scanner room let them know

   • We will have them put on scrubs when we get over there.

   • They should use the bathroom if needed before getting in

   • Give them a spiel about head motion and how we will monitor it and give them feedback

3. Show them the restroom and tell them to change into scrubs

4. If the MRI Tech is not there yet go find them

5. Take everything out of your pockets and remove any metal

Monitors in MRI Suite

From Left-Right facing the monitors

• Far right tiny monitor near the shelving is the button box control (ResponseMonitor)

• The second right monitor is for Eyelink (EyetrackerMonitor),

• Middle monitor is for motion tracking (MotionMonitor)

• Second from left is the monitor you set up your experiment and it’s shown to the participant (ExperimentMonitor)

• Far left monitor is the MRI Technologist monitor (MYOBMonitor)

  • Do not touch this monitor unless specified by MRI technologist!

Setup Eye Tracker

Connect Power Cord

1. Find the Eyelink cord inside the pull-out drawer under the desk on the right side under the EyetrackerMonitor.

   • It’s a power cord with big box on one end and a VGA on the other.

2. Stick the VGA part through the tube to be connected to the Eyelink on the other side (will have green tape on the cord). Then find the power cord that is marked with green tape to be connected to the box side.

3. Go into the MRI room and connect the cord to the other cord with green tape

4. Now push that connection back all the way into tube, we don’t want any metal in the MRI suite.

Position Eye Tracker

1. Go to the back of the MRI machine and move the black cardboard away and then roll the screen away from the bore.

2. Take the cap off the eye tracker lens.

3. Pick up the eyetracker mount carefully and place the mount within the white masking taped area.

4. Move the screen back onto the black tape on the ground.

Turn on Eye Tracker Computer

1. Turn on the eye tracker computer

2. Select EyeLink startup

Setup Experiment Computer

1. Turn on the monitor in the MRI machine

2. Login to the computer

   • User: cabi_users

   • Password: cabi30318

3. Open our study folder

User Experiments / Engle / ONR fMRI

Setup Button Box

1. Connect the button box (or ask MRI Technologist) using the optic cable inside the room with the MRI. We are using the right button box.

2. Turn on the ResponseMonitor. The power button is in between the two cords connected to the ResponseMonitor.

3. Once the ResponseMonitor boots up, select the input. Have the ResponseMonitor select the input automatically (it should be the right button box) HHSC-1x4-CR

4. Click on output mode – select an output mode as HID_KEY_12345

5. When the MRI tech is ready for you, show how the button box works to the participant and show them which buttons they will be pressing for the experiment.

Setup Motion Tracker

1. On the MotionMonitor, only use the stylus - do not use your finger!

2. Go to settings. Change fMRI motion threshold to 0.3.

3. Under BRAIN SIZE turn ON Respiratory Filter

MRI Tech

While you are doing all of these steps the MRI Tech will be setting up the particpant on the scanner bed

Finish Setting Up Eye Tracker

Once the participant is in the scanner you need to finish setting up the eye tracker and verify that everything looks fine

1. Make sure the pupil is clearly in view, not occluded by the head coil

   • If it is occluded, instruct the participant to move more to the LEFT. But they need to be in a comfortable position otherwise they will just eventually move back.

2. You should not have to adjust the focus on the camera, but if the video on the EyetrackerMonitor is blurry, you will have to adjust the focus manually by turning the lens of the camera while it is inside the MRI.

1. Adjust tracker square box (on computer) to capture the eye by clicking the center of the eye with the mouse

2. Adjust pupil and corneal values so that the pupil is filled in completely with the dark blue and that the white dot in the center of the eye is filled in with the aqua color.

   • Corneal values: +/-

   • Pupil values: Up and Down Arrow keys

Scanning Procedures

Whole-Brain Scans

Using the Microphone

There is an on/off button on the left bottom.

On the right there is a toggle.

Push down the toggle to speak and hold it down while you speak. Don't speak too closely, it is loud for the participant!

Make sure you turn up the sound so you can hear them

When you are done always turn down the sound so you can’t hear the noise from the MRI during scan.

1. Ask participant if they can hear you, and tell them we’re going start the structural scan and they need to lie as still as possible for 8 minutes. The MRI technologist will then begin the structural scan.

2. They can keep their eyes closed but do not move their head, and they should not fall asleep. Or we will have to restart.

3. During this time, pull up any of the 3 task and run it, enter subject ID as 0 just to see if it skips eye tracking set up. If it does, just restart the eye tracker while the structural scan is going on.

4. When the structural scan is done, unmute the mic and check in on the participant. Tell them there will be a loud noise for about 10 secs to finish up with the scan.

5. Now, turn on the experiment display screen, so the participant can see what you see on the ExperimentComp.

6. Have the MRI Tech make sure the lights in the bore are turned on to level 2

Functional Scans

1. Make sure to TEST the button box to make sure it is recording the participant responses.

   • Open up the Notepad file on the desktop titled keyboard&button_check. Ask the participant to first press down with their index finger. It should register as 2 on the notepad, then ask them to press down on their middle finger and that should register as 3. If it doesn’t you would have to restart or replug button boxes.

Follow these next steps for each task: Rest, 1-back, 3-back

Start Task

1. Run the E-Prime task

2. Subject ID prompt: 18###

3. Save the eyetracker data as the same but with an addition at the end to indicate the task. 18###r or 18###1b 18###3b

Calibrate Eye Tracker

1. Tell the participant to focus on the circle as it moves on the display

2. Press 'C' to start calibration

3. Press the spacebar when you are certain they are focusing on the center circle

4. The calibration will continue automatically from there. However, if you need to continue the calibration manually because it is not moving on continue to press the spacebar for each circle

5. The calibration on the EyeTracker Monitor should look like a cross of 5 fixations

6. Press 'V' to start validation

7. Again press the spacebar for the first circle and so on

8. The error values should be quite small <1 or <1.5 is okay

9. When validation is done click “enter. ” Click on “o” key, you will get the instructions for the task.

Read Instructions to Participant

1. Read the instructions to the participants. Get verbal confirmation that they understand the task. There are several instruction screens

2. The last screen will remind them to keep as still as possible. Press the spacebar to move on to the fixation screen

3. At this point, you can tell the MRI tech to start the scan.

During the Task

1. Check the MotionMonitor to monitor their movement

2. During the experiment, also make sure that the ResponseMonitor is showing that the participant is responding on the button box.

3. Make sure that the participant does not fall asleep by looking at the EyetrackerMonitor and making sure that their eye is open.

After the Task

You can do this after the task or just before starting the next task

1. Give them feedback on how much they moved (good job, a few spikes, etc.) If they did well, tell them “great job, that’s how you need to be for the next runs/blocks”.

2. You should give them feedback on their motion after every task

3. Then keep encouraging them. It is tiring to stay still in a loud noisy box.

4. Make sure they are comfortable and that they can continue.

5. If not ask if they need a minute to rest, to wiggle their toes/body to help them stay awake while in the scanner.

High-Res LC Scans

1. When they have completed all 3 functional scans (rest, 1back and 3 back) there are few more structural scans to be done.

2. Turn off the ExperimentComputer screen, clicking on the blue button on the horizontal white box.

3. Talk to the participant to tell them there are a few more scans but they can relax and close their eyes BUT they should not move their head still. The scans will take 15 mins.

Final Steps

Upload Data to SharePoint

While the high-res LC scans are being done, you can upload the data to SharePoint

1. Create a folder for the participant's data

ONR fMRI / Subject Data / 18###

1. Then go into each task folder (rest, 1back and 3back) and into the subfolder data and take the EdataAid file (with the icon) and the -EXPORT file.

2. Then go into the subfolder called Results and take the corresponding edf file. (3 files x 3 task = 9 files total)

3. Move them into the Subject’s folder

4. Then click on the Sharepoint shortcut in the ONR_fMRI folder and sign into your GT account and upload the whole subject’s folder to Sharepoint in data/subject

5. NOTE: if the files won’t upload, go to network settings on the computer and turn on or off WIFI: eduroam. Sometimes Wifi works better, sometimes LAN works better.

Clean Up

1. After the structural scan is over, go in and greet your participant and thank them.

2. Shutdown the Eyetracker from the screen. Turn off EyetrackerMonitor by clicking shutdown host on the monitor. DO NOT PRESS THE POWER BUTTON ON THE COMPUTER.

In the MRI Room

1. Move the display screen and move the eye tracker back to its home and put back the cap on the lens GENTLY! You don’t want to move the focus

2. Unplug the eyetracker cable from the inside and push it back out through the tube.

In the Control Room

1. Unplug the eye tracker power cord and put it away.

2. Turn off button box by pressing on the button deeply at the button of the ResponseMonitor.

3. Close the MotionTracking monitor

End Session

1. Make sure they don’t leave before the MRI Technologist pulls up their structural scan on the MYOBMonitor. The participants can take pictures with their phones.

2. Ask them to check if their address is correct for payment.

3. Show the participant the way out.