If you are using the projector:

1. Replace the flat plastic board behind the scanner with the one in the projector closet.
2. Put the mirror on that board in the square designating its correct position
3. Turn the projector on by turning on the power strip. If this still doesn’t work, then look at the back of the projector to see if the switch is in the On position. In the control room, change the “ceiling monitor” and “projector” options so the blue light is at 7.
4. Get the projector screen and carefully attach it to the back of the headcoil.
5. Unscrew the mirror, and carefully put it along with the 4 screws to the side. Then go get our mirror from the Gardner Lab drawer and 4 screws, and screw it into the head coil.
6. Make sure in mgl your screen displayName is set to “fMRIprojFlex”

If you are using the LCD:

1. Turn on the LCD (button is labeled, on the left side of the television)
2. Retrieve the HDMI extension cable from the Gardner Lab drawers
3. Get the HDMI to DVI converter from the little plastic box of dongles and converters that sits next to the scan console
4. Connect the LCD’s HDMI cable to Oban using a HDMI to DVI converter and the extension cable
5. The ‘somato’ screen is setup to use this monitor, but there is no gamma table/calibration so be careful if you’re doing low-level visual stuff, you might want to fix this….

There are two main things to take care of here. Basically, Oban needs to get triggers off the scanner so it can do stimulus timing, and it needs to get responses from the subject. Getting this right requires (i) all the correct cables are connected correctly and (ii) the FORP (fiber optic response blah… the thing we use to get responses) is configured properly.

The Little Black Box

On top of Oban lives a little (medium sized) black box, that has a BNC input and (I believe) a DB9 input. The BNC gives the scan triggers. The cable is labeled “slice trigger out”. The DB9 (or whatever it is) connects to the FORP and is labeled as such. Both of these need to be plugged into the “little black box” (LBB) for Oban to receive the relevant information. The little black box then needs its USB output to be plugged into Oban. Occasionally, Oban forgets the little black box exists, in which case you won’t get triggers or responses. If this happens, unplug and plug in the little black box, or just try restarting Oban.

In short:

1. Make sure the BNC slice trigger cable is plugged into LBB (*THIS STEP NO LONGER NEEDS TO BE DONE EACH TIME)

1. Make sure the DB9 cable from the fORP is plugged into the LBB

Scan Triggers

Underneath the console (the computer where you prescribe scans) is a T-junction BNC cable, normally with the bottom of the T disconnected. We just need to connect our cable that goes to the LBB (little black box) to the bottom of that T-junction. The cable that goes to our little black box (henceforth: LBB) is marked with orange tape. Connect this to the T-junction and we’re good. Disconnect the bottom of the T-junction after your session, because unfortunately the T-junction is not as good as we hoped and sometimes it steals other people’s triggers if we keep our cable connected.

fORP (Responses)

1. Take the response box you want and plug it in (inside the magnet room). The button boxes plug into a cable out of which red light shines… it’s an optical system… cool.
2. The ‘fORP’ box sits on top of a computer under the main console. Go there now.
3. Press the dial on the front of the fORP once… press again to say you do want to change the configuration
4. When navigating the fORP menu with the dial on the front, choose autoconfigure → serial → ASCII12345.
5. Check the serial number shown on the display matches the serial number of the button box in the magnet room

If autoconfig doesn’t find the appropriate button box, you can do manual config. You’ll just need to know the serial number, which should be printed on the response box (we often use ‘HHSC-2×4-C’) and choose it from the menu, then choose Serial → ASCII12345 like normal.

Oban Setup

1. Set the input on the stimulus computer to HDMI2 for Oban.
2. Grab the white mac keyboard. Disconnect the mouse from the computer and plug it into our keyboard.
3. Login using our lab’s standard password.
4. Open MATLAB.
5. To get the stimulus to start at the proper time, do things in this order:
   1. Get your functional scan ready to go, but instead of clicking “SCAN”, click the little button next to the scan button and you’ll get a dropdown menu. Choose “PREP SCAN”. The scanner will make some noises and throw off some triggers.
   2. Start your stimulus code on Oban. It should do some stuff, open the screen, and then pause and say “waiting for backtick”.
   3. Now click “SCAN” on the console.
   4. After 16 volumes (the calibration frames), your stimulus should start. If it doesn’t, get extremely tense, swear a lot under your breath, and refer to the other parts of this document that explain how to get scan triggers to Oban.

Scanner bed

1. Put the bedsheet on the scanner bed, small cushion in the head rest (maybe a neck pillow), leg rest thing, and cover the head area with a pillowcase.
2. Tell the subject to put earplugs in, and have them lay down on the bed. Make sure the head is fully in the coil.
3. Put pillows on either side of the head between the coil and the head to ensure they’re completely secured in position.
4. Put arm pads in between the edge of the magnet and the subject’s arms
5. Check that the mirror lets the subject see what they need to see
6. MAKE SURE SUBJECT CLOSES EYES BEFORE YOU SHINE A LASER ON THEM
7. Ask the subject to close their eyes and do alignment stuff. Hit “landmark” button when the laser cross is right between the subject's eyebrows.

Controller

1. Write the subject id (e.g. ‘s0350’) in the LastName field.
2. Write the subject id and experiment name (e.g. ‘s0350@jlg/mglRetinotopy’) in the patient name field
3. Fill in the subject’s weight field or the magnet will get unhappy about not being able to calculate SAR limits
4. Write your own SUNET ID in the scan operator “First Name” field
5. Get the protocol – it will be in the Neck area under Gardner Lab Protocols. Regular protocol is mux4. Also grab the 0.9mm sag T1 if you need high quality anatomy.
   1. typically :
      1. 3-plane localizer
      2. T1 1.2mm/ T1 0.9 mm
      3. HOS shim
      4. mux4 CAL_ssg
      5. mux4 2.5mm_ssg

1. Double click on the T1 anatomical protocol, hit save and accept.
2. Shift the squares so that they fit around the brain. [V IMPORTANT DO NOT FUNCTIONALLY IMAGE THE THUMB!!!!]
3. Prescribe your MUX scans. It is important to prescribe Mux scans PRIOR to shimming, as this will mean when you shim it will optimize for the shim for Mux.
   1. Prescribe Mux Calibration. Roughly position your slices in the center of the brain (there should be 13 of them for the Mux 4 2.5mm scan). Then change n(slices) to the Mux factor (normally 4) times whatever you had (eg: 4 X 13 = 52 for our workhorse 2.5mm sequence). Now you can see your actual coverage and make sure everything is positioned right, that all the brain you want to see is covered and that there’s a little headroom (a couple of slices above the edge of the brain). BEFORE YOU SAVE THIS, CHANGE N(SLICES) BACK TO 13 (or whatever it was originally… 10 for the 1.6mm sequence…).
   2. Prescribe the real Mux EPI scans. Without changing anything, we will copy the slice prescription from the calibration scan to the actual Mux EPI scans. Double-click to setup. Click ‘GRX’, then ‘RX–> RX’, then double-click the Mux calibration prescription. If you need to change n(volumes), go into the “multi-phase” tab. N(volumes) is referred to as “phases per location). You should pick however many you need for your stimulus/task, and then add 2 X Mux Factor (eg… normally 8) more for the calibration frames at the start of the scan.
4. Prescribe the shim by opening and saving it (no need to actually prescribe anything, it will know to shim to the Mux now you’ve prescribed it). Run the Shimming. [That felt good right? Rerun it a bunch of times until the predicted and actual RMS are very close, like, below 25 and within 0.5 of one another → for each extra shim, always choose “add to same series”, don’t make a new series]
5. Run Mux Calibration Scan
6. Run Mux real deal functionals as many times as you need them (duplicate them to get more with the prescription you already did).

1. Do not enter numbers only as subject id (e.g..25). This will send your data to cni's “unknown folder”. You'll have to ask Bob to get the files back for you.
2. Shim Failure: If the shim fails and you don't want to restart your scan click the hammer/wrench button (top left) and open the service manager and open a C shell. Type: “fixshims” and you should see the shims all go to 0 (or approximately 0). Type it twice if you aren't sure. Once that's done redo your localizer scan and go into the advanced setup options and turn the shim ON (from auto). Then run your remaining scans as normal.

“No matching processes belonging to you were found”

1. Quit digIO and start matlab again.

Projector not getting signal from Oban

1. Check that the orange cable at the back of the projector is plugged in. Check that the orange cable is plugged into oban.

Reboot the projector.

To get the eyetracker screen visible on the MRI

1. Press the buttons on the black box with the lights to get the eyetracker screen on the screen above
2. Then, press some buttons on that box dangling behind to get it back onto the MRI

mglDigIO not finding connection — or something about “cannot find mglStandAloneDig”

1. Check the cable connections
2. Unplug the black cable from the right of the little black box on top of oban and plug it back in
3. Quit matlab and start again: type mglDigIO(‘init’)

fMRIProjFlex screen looks out of focus

1. Someone may have messed with the focus / zoom on the projector. Very carefully try twisting different parts along the projector lens and see if that improves the focus.

Eyetracker wobbly

1. There’s a screw that attaches the eyetracker to the snake thingy that sometimes gets loose. If so you may need to just unscrew it, disassemble the snake thing, and rescrew the eyetracker firmly back onto the snake.

Eyelink says “OPTICAL LINK ERROR” as soon as the scanner starts.

1. Unknown how to solve it.