Lab Manual:Scanning

Scheduling Subjects

For recruiting see the recruiting section of the manual. If you are using sona, there is an option to recruit only participants that do not have metal implants (however, you still need to go over the screening forms).

Before contacting a potential participant, check the SPAN Lab Gray List, which documents potentially problematic participants. You can access this list by logging into Google Docs and viewing the SPAN Lab Scanning Participant Gray List:

go to http://www.google.com/documents

• name: "spanlab"
• password: balnaps
• when done, logout

Make sure to screen all of your subjects before the scan using the magnet screening form and the span lab screening form.

You must also have your subject check the magnet screening form at the scanner the day of the scan, even though you already went over the form on the phone.

Add the event to the lab calendar:

go to http://www.google.com/calendar

• name: "spanlab"
• password: balnaps
• when done, logout

Scanning

Before leaving for the Lucas Center you’ll need:

• the right study questionnaires
• participants’ screening forms
• consent form (2 copies)
• Brian’s log book
• human subjects payment sheet
• cash
• subject phone #’s (just in case)
• your card key

Meet your subject

• If scanning before 5 pm, meet your subject out on Welch Road and provide him or her with a parking pass (located in folder near window between the restroom area and the scanner computer room). The pass is good for spaces in the Oak Road Parking Lot, located across Welch from the Lucas Center and accessible from Pasteur Drive.
• Check that the magnet screen is okay
• Review the consent form with your subject
• Get him or her a locker, have your subject remove all metallic objects from his or her person – also make sure wallets don’t go into the magnet room (the magnet will demagnetize credit cards)
• Check to see if the subject needs to be fitted with scanner-safe reading glasses. These are located in a black case above the eprime computer.

Set up in magnet room

• head coil, mirror, bite bar set up, pad, sheets, earplugs
• turn on projector

Refer to task-specific training document for training script

• Emphasize understanding of the task, stimuli; have the subject do a practice run if appropriate.

Bite bar fitting

• Explain concerns about head motion – “When inside the scanner, please remember that it is important to keep your head motionless. To make this possible we will make a bite bar with an impression of your teeth.” It helps to show them with a ruler or your fingers just how little movement can be corrected by the software – people don’t realize what ‘try not to move’ really entails and are probably thinking on the scale of a half inch rather than a millimeter or two.
• Explain the position that they will be in when inside the scanner (with head tilted back slightly)
• Take an impression of his or her teeth. Hold the bite bar yourself and make sure it is straight and that the participant’s head is tilted slightly back when they bite down.
• To make a bite bar, take a half-teaspoon of the grey putty and a half-teaspoon of the red putty, kneed with your fingers until a uniform color, and fit over the bite bar form. The putty and bite bar structure is located in the drawer labeled “Knutson” over by the medical prep bed area and sink.

General set-up

• Enter info into Lucas logbook (located to the left of the magnet computer on top of some audio equipment).
• Have your subject fill out a consent form, task-specific pre-scan questionnaires, and a pre-scan screening form if it has not been completed already. Give the subject an extra copy of the consent form to take home.
• Enter info into Brian’s logbook (name, gender, ethnicity, subject number, task, exam # [located on top RH side of the magnet computer screen after the scan begins], a space for I & S values, and winnings after they have completed the task, as well as general notes on the scan).

Prepare Signa (GE Operation Program) on the Scanner Computer

You’ll need to set up the patient profile (in the RX manager on the scanner computer) before the landmark is made.

• Click the picture of the scanner, then “NewPt”
• Complete the following fields using info from the screening form:
• Patient ID: B Knutson <enter>
• Operator: Your initials
• Normal Mode
• Patient name: [First Last] <enter>
• Weight (lbs): [xxx] <enter>
• Exam description (head and participant’s DOB): [head DOB mm/dd/yyyy] <enter>
• Click the head graphic
• In the list of protocols, select your protocol
• If it’s not there, click “Site” and try again

Getting the participant set up in the scanner

• Double check for metallic objects. NO metal can enter the scanning room (including bobby pins, small clips, coins, underwire bras, etc). Most jeans are okay provided they don’t have unusual metallic decoration. Belts are not okay, even if the subject claims no metal in the belt. Refer to your scanner training materials for comprehensive safety information.
• Remind the participant to use the restroom.
• Have the participant put in earplugs (remember to speak loudly and clearly from here on out).
• Have the participant lie down on the scanner table, and ask him or her to move up so that his or her shoulders are flush with the head cradle posts. Place a pillow underneath his or her legs, place small pads between the subject’s shoulders and the head cradle so that it doesn’t dig in and make them uncomfortable, and ask if he/she wants a blanket.
• Hand the participant the button box, tape the squeeze ball to his or her shirt using the tape located next to the projector, and explain both. The squeeze ball is there in case of emergency or if they just want to get out – they can squeeze it, which will set off an alarm in the scan room. The alarm box is next to the scanner computer; press reset to turn it off.
• Explain the sequence of scans (pre-task localizers, # of sessions of task, post-task structural). Ask if the subject needs you to review the task itself.
• Position the bite bar.
• Make sure the participant is completely comfortable and make adjustments as needed. Do not continue with the scan unless the bite bar setup is straight, the participant is comfortable, and the head coil slides into place without trouble.
• Align participant (press ‘align on,’ move scanner bed inward until crosshairs are right above eyebrows, press ‘landmark’)
• Slide head coil into place and then check that the participant can see the mirror.
• Tell the participant that you will communicate over the intercom and then move participant into place.
• Check to make sure the task screens are centered once the subject is all the way in. The easiest way to do this is by creating a test screen with a representative slide from your task. Ask the subject whether they can see the top and bottom, and check to make sure it’s in focus and centered. Make adjustments as necessary.
• Now you’re ready to go! Head back to the scanner computer.

Collecting Physio Data

• Note: If you are going to use the physiology equipment you should probably contact Anne Sawyer to get an overview of how to treat the equipment.

The bellows belt:

• This is the black rubber tube with a section in the middle that looks like an according. This belt is used to collect respiration data.
• The subject should wear the belt around their abdominal at the place that expands the most as they breath. This will depend on the subject but it will either be the belly or the chest.
• Fasten the belt with the Velcro on the ends of the belt. You should fit the belt with some tension on the bellows but not so much that it will not expand when the subject breaths.

The pulse monitor:

• This is the white clasp that goes over the subjects finger to monitor the subjects pulse.
• The subject should wear the clasp on the index finger.
• Important Note: The subject will not be able to use the button box with the had that the monitor is on for two very good reasons:

1. the wires of the pulse monitor need to be kept away from the wires of the button box.
2. If the subject moves his/her hand in response to the task, this will corrupt the pulse signal and render it meaningless.

Computer settings:

• On the user CVs page of your scan protocol:

1. Set the xfer CV on that page to 45 if not already using 31.
2. Set the physio monitoring option to on

• Doing this will generate a file called Pfile.physio after the scan concludes. That file has cardiac trigger info, expressed as sample numbers at which a trigger occurred (40 Hz sampling rate), followed by -9999, followed by respiratory data sampled at 40 Hz. There is a script that will read this data on Gary's website in fmriutil, called readphys12.m.

Scan Procedure

• Make sure scanner is in research mode
• Click on “scan modes”
• Make sure “Research” is selected (NOT clinical! If the scanner is in clinical mode, it will not run spiral in-out research sequences.)

Scan #1 – 3 plane localizer (~40sec)

• Ask subject if he can hear you, and adjust volume with knobs on top of keyboard
• “ear” → what we hear
• “mouth” → what participant hears
• Press the bar at the top of the keyboard to turn the intercom on so that the subject can hear what you say. Keep in mind it’s like a walky-talky – you won’t be able to hear them while it’s pressed, and they can’t hear you if it’s not pressed. Tell subject:
• “OK, we’re going to do three very short structural scans that are each under a minute. Please remember not to move your head during or in between scans. You’re going to hear some clicks in just a minute.”
• Turn the lights down
• Select: “3 plane local”, then “view edit” (alternatively, just click “3 plane local” twice)
• Press: “Save series”
• Press: “Download”
• Press: “Scan”
• Write down exam number in the lab scanner notebook – to find the number, look at the scan window in the upper right corner (e.g, Exam # 4527).

Scan #2 – Axial Inplane (~2min)

(The inplane scan is dependent on your ROIs and what coverage of the brain you would like during the scan.)

• Select “axial plane,” then “view edit”
• Press: “Graphic RX” → this will bring up Inplane Anatomy
• Click on the sagittal image once with the left mouse button. Now you can again click on the left mouse button and drag the slices.
• Make sure the 24 slices cover from mid-pons to top of brain. If it doesn’t all fit sacrifice the top of the brain first.
• Zero out “P/A center” and “L/R center” – everything except the I & S values should be zero.
• Write down S-value and I-value in log book (these refer to the inferior and superior coordinates for the slices)
• Press “Save series”
• Press “Download”
• If the “move to scan” button is blinking warn the subject (“you’ll feel a small shift in the table before the scan begins”) and then press it.
• Press “Scan”

Scan #3 – Shim (~2min, including two 30s scans)

• The shim tries to homogenize the magnetic field. The field was OK without a head there, but the head has all kinds of bad magnetic stuff going on. The data looks cleaner if we can try to account for this before getting functional data.
• Press “Save Series”
• Press “Okay”
• Press “Download”
• Pres "Scan" (this is new as of September 2009), 9 sec scan
• Set the oval around head as closely as possible in the axial and sagittal views.
• Press “Calculate Shim.” The RMS should be =<10, >15 is not okay, and you should move your ovals until it’s around 10.
• Press “Done”
• Press “Scan”

Scan #4 – Functional scan – run 1 (the length is the duration of your task)

• Select “sprlio”, then press “view edit”
• Click on Usr CVs, check the # of TRs to make sure it’s correct
• Click “Graphic Prescription”
• Select “Erase All”
• Click “Copy RX”
• Select the axial inplane
• Click “Save Series”
• Click “Download”
• Make sure the task is ready on E-prime desktop
• Remind subject of the task specifics (refer to training doc for the task)
• Tell subject: “The task is about to begin. Please try not to move your head. You’ll know the task is starting when you see the screen change…”
• Click “Prep Scan”
• Start Eprime, but don’t advance past the last instruction screen
• Press “Start Scan”
• When the white “Stop scan” button lights up on the keyboard, quickly press <space bar> on the E-prime desktop keyboard (within 24 sec of pressing the green scan button) to start the eprime task.
• If the scanner doesn’t trigger, stop the scan (press the “Stop Scan” button at the top of the keyboard) and try hitting prep scan again, followed by “Start Scan” and then starting Eprime.
• If the scanner still won’t trigger despite repeated attempts, you can manually trigger the scanner by changing your user CVs from 1 to 0 in the “External Something” or “Trig Mode” What is it called exactly? – check this when next at scanner. line. This time around, the scanner will trigger as soon as you press “Start Scan.” This means you need to press space bar on the Eprime screen where you’d normally trigger at the exactly same time that you press “Start Scan” on the scanner computer. This involves some contortionist movement to get the keyboards as close together as possible so that you can try to hit them both at the same time.

If you have a second block:

• Click “Prep Scan”
• Start Eprime
• Click “Scan”
• Same goes for a third block, et cetera.

When scan is complete, tell participant, “Okay, you’ve just completed that session. Please remember to keep your head still while we set up the next scan.” Do not comment on the participant’s performance.

Scan #5 (or higher) – 3D volume (10min 42sec)

• Tell subject: “You’ve finished the last session of the task. Try to remain as still as possible, but now you can relax during the structural scan. This scan is about 10 minutes long.”
• Select “3D volume”, then press “view edit”
• Press “Graphic RX” – the RX varies between tasks
• Click on the axial image once with the left mouse button. Make sure the subject’s head is contained within the box. If it’s not, you can again click on the left mouse button and drag the box so that the subject’s head is inside it.
• Press “Save Series”
• Press “Download”
• Tell subject: “The structural scan will start in a few seconds.”
• If green light is blinking on keyboard (move to scan button), warn subject and then press it before pushing “Scan”
• Press “Scan”

Ending the scan

• Tell subject: “Okay, we’re coming to take you out of the magnet.”
• Press “End Exam”
• Take your subject out of the magnet, let them gather belongings and use the restroom.
• Print pictures if participant wants them:
• Click the browser icon (picture of screen)
• Click “browser” on left-hand side
• Select current patient in left-hand window
• Select series (3Dvolume)
• Click “viewer”
• Use slider to find a good slice to print, and also use “Format” options to display 1, 9, or X images at the same time
• Hit the Print Screen button (upper right of scanner computer). Click OK when a window pops up, and cancel it when it pops up again.

Post Scan

• Record winnings the subject made in each block and/or task in Brian’s logbook.
• Have the participant fill out the appropriate questionnaires and affect scores, make sure you have all the surveys you need (NEO, PANAS, EHI). You should always give the EHI (Edinburgh Handedness Inventory).
• Exit Form: Have the participant fill out Lucas post-scan survey form.
• Pay the participant and have him or her sign the payment sheet.
• Thank the participant, make sure they have everything, and help them out of the Center.

Moving Files

Move the P-files and structural images to a safe place; normally to the subject’s experiment directory on dmthal. To move the files, open the FTP program (e.g., Secure FX) on the computer in the room just inside the scan suite door (that’s the one with the printer, the computer is to your left as you enter). Connect to lcmr (the scanner computer) as well as to dmthal. You should already have a window open for “local,” the computer you’re on. With these three windows open, move all scan files (P files, anything else present) from lcmr to local, then from local to your experiment folder on dmthal. There are folders for labs to place their data on ‘local.’

To get the anatomical files, open Get X11. Sort by date and click “List Exams.” Scroll to your subject’s exam (usually the most recent exam), select it, and click “Get Exam.” It should show up in the local “scratch” folder. Move the file from the scratch folder and into your experiment folder on dmthal.

Moving behavioral data to a safe place:

Use SecureFX to move the Eprime .edat AND .txt files from the eprime computer to dmthal (or appropriate computer). You can do this from the Eprime computer.

Cleanup

• Clean up the scanner room.
• Turn off the projector.
• Place Lucas post-scan forms in the bin on the side of the Eprime computer desk.

After session

• Record subject ID, exam #, gender, age, ethnicity, scan prescription start/end points, and any other relevant info (e.g. amount $$ won) in the note file in the subject’s data directory. (Basically, replicate your entry into the lab scan notebook.)
• Scan data should be pre-processed within a week. Brian and the lab coordinator should be informed if there are data integrity issues.

Scanner Troubleshooting

If you can’t solve a problem, consider called the lab manager, Brian, another knowledgeable member of the lab, Anne Sawyer, or Gary, in that order. Be careful about calling people late at night; in particular it’s not a good idea to call Anne or Gary after 10pm unless it’s a medical emergency.

I can’t find my scanner protocol file.

Rarely, ‘upgrades’ to software delete protocols/routines, usually if they haven’t been re-saved as directed
by Anne.  You can use another recent experiment’s lab protocol and simply modify the number of TRs per run
when you pull up the Graphic RX screen during the task sequences. 

The scanner isn’t triggering.

Start the Eprime script again, prep the scan, and try again.  If this doesn’t work, see the 
paragraph on manually triggering the scanner in the scan protocol section, above.

The scanner gives an error that the subject comfort level is warmer than normal and will not scan.

Wait for a while and try again.  The temperature readings in the scanner are often faulty.

Eprime gives an error about the Display and will not run the experiment.

Restart the Eprime computer (pwd: lucas15scan) and try again.  This is a Windoze problem.

Part of the participant’s brain isn’t showing up correctly on the screen.

This is called “dropout” and is often caused by hair clips and bands that made it in there with the 
subject.  Pull your subject out and check.

Scanner won’t shim.

This requires troubleshooting by the experts.  You can try running your scan anyway, though you may want 
to see if the subject is willing to come back another time.

Paying Your Subjects and Finishing Up

Get cash and/or checks and payment forms from the lab coordinator. Make sure the subjects are US Citizens with social security numbers (needed for grant reimbursement). Talk to the lab manager before running someone who is not a US citizen. After paying the subject and making sure the payment form is filled out, go onto the spanlab google account and open the hs payment spreadsheet. There, record the date, amount, and study in the appropriate columns. This allows us to easily total up cash payment advances that we get from grants.

If you experienced any problems with the participant (moved too much, arrived very late, etc), it is a good idea to document this. You can add this participant to the SPAN Lab Gray List. Visit http://www.google.com/documents to add the participant to the list.

• login:spanlab
• password: balnaps
• Click on the Gray List document to edit and save any changes.
• Be sure to log off when you are done.

Now that you’ve finished collecting data, you can move on to data analysis…