How to scan - theunissenlab/lab-documentation GitHub Wiki

Table of Contents

  1. Starting up the scanner

  2. Setting up peripherals

  3. Sequence of getting the subject ready

  4. While scanning

  5. Localizer Scanning Protocol

  6. Shutting down the scanner

Starting up the scanner

If you are the first person of the day:

  1. Press the blue “System Start” button. This will start the Siemens console as well. No need to start the desktop!
    1. MrVCheck message: Findings occurred, check logfile. [OK]
  2. Wait until 3 beeps or until the connection icon in the bottom right is not crossed with a red line. The scanner is ready then.
  3. Do a QA scan using the phantom and the 12 ch head coil
    1. PatientName: User_QA_Startup_[your name]_YYYYMMDD
    2. User_QA → 12 ch head
    3. Head First Supline
    4. Add the two sequences (localizer, something else) using << and scanning will start automatically.
    5. Remember to note that you did the Startup QA scan in the notebook.

Shutting down the scanner

If you are the last person of the day:

  1. QA scan of the phantom using the 12 ch head-coil
    1. PatientName: User_QA_Shutdown_[your name]_YYYYMMDD
    2. User_QA → 12 ch head
    3. Head First Supline
    4. Add the sequences using << and scanning will start
  2. Take the phantom out
  3. Shutting off the scanner:
    1. Turn-off the siemens console (takes about 10 min)
    2. System Tab → End Session → Shutdown System
  4. Turn-off the scanner
    1. Press the blue button “System Shutdown”

Setting up peripherals

  1. Connect the stimulus computer
    1. VGA for projector
      1. 2019 note: You have to use an adapter because the VGA port on stimmy is not working
    2. USB for TTL (Orange label Laptop FORP), connect this to the front of stimmy
    3. FOC for Audio if you are playing sound
      1. One end connects to a port in the back of stimmy
      2. The other end connects to a port in the back of the 32 headphone digital labelled “IN” (not “OUT”!!)
  2. Turn on Avotec projector if not already.
  3. If you are playing sound:
    1. Turn on the 32 channel headphone digital
      1. Press buttons in order: 2, 3 (TURN OFF IN REVERSE ORDER!)
      2. Select Digital I/O
      3. Memory → Digisens2 (Turn until select) → Select by pressing the button B then B
      4. I (CT) usually then press RTA which shows sound amplitude (?)
    2. Check that things work
      1. Go to Sound on stimmy and click Test Sound. Make sure sound is actually playing when you click Test Left and Test Right.
  4. Turn on the BIOPAC and Pulse oximeter. Turn on the power strip, then press buttons in the order labelled (1, 2, etc.)
  5. Video splitter and switch
    1. All to LAPTOP (Press 1 (Projector) and then 4; Press 2 (Display Monitor) then 4)
    2. Press 3 instead of 4 to display the eyetracking/physio computer
  6. Eyetracker/physio PC
    1. Physio
      1. Open the ACQ.-Software (file labelled gallantlab.acq on the Desktop)
      2. Click “Start” at the top
    2. Eyetracking Avotec
      1. Start the Voltage Pro Shortcut Software to get the TTL
        1. Error1: DDL versions does not match SDL versions [OK]
        2. Error 2: Previously used board not found [OK]
        3. Load Parameters → [something parameters it’s the first one that pops up].prm → Open
      2. Then start View Point EyeTracker Software
        1. Set up recording:
          1. Check the box: File → Data → Include Events in Data File
          2. File → Data → New Data File
        2. Press “RECORD” to check if recording.
        3. Go to Eye A (or B if you are doing the right eye).
        4. There are multiple ways to do eyetracking, I (CT) usually do Pupil for feature method but you can also use Glint-Pupil vector.
        5. For Pupil, draw a box around the eye and hope that ViewPoint can find the pupil within that box. Play around with contrast/brightness/scan density etc. until it looks stable.
  7. TTL switches
    1. Flip on “Laptop” and “Eyetracker”.
    2. EVERYTHING ELSE SHOULD BE OFF
  8. Make sure FORP Power Cycle is turned on.

Important Note

Laptop TTL should only be connected after the subject is in the machine and should always be connected to one of the front USB ports

  • the back USB ports are connected to BIOS stuff and sometimes the Laptop TTL USB sends over random signals related to magnet hardware (but not TTL) and this causes stimmy to get stuck on the BIOS page for a long, long time
    • This only occurs if you plug it into BIOS update USB port (I think) that is clearly marked -TZ

Sequence of getting the subject ready

  1. Have them put in earplugs
    1. If you are playing sound, red is right ear and blue is left ear. Also go and play a sound from stimmy to make sure 1. everything works and 2. it’s loud enough. Make sure you ask the subject if it’s loud enough.
  2. While they do this, put the 32 channel coil in place and put their headcase in position
    1. Don’t forget the black shim
  3. Also get the mirror and eyetracking stuff and put the eyetracking camera on the mirror
  4. Then have them put the breathing thing about two fingers distance below their last rib. Have them put on the belt, make sure to tell them that the belt goes over the breathing thing!! Make sure they put it on tight, because it will become looser when they lie down.
    1. Exhaling before putting on the belt helps tightness
  5. Subject lies down in scanner, put top headcase on top and secure them in with the top coil.
    1. Make sure each side “clicks”!
    2. Plug in all the plugs, the scanner will say “32 ch coil” or something if it’s done correctly
    3. 2019 update: As per Ben’s email, the plugs are a bit loose so gently guide each plug in, lift it a little, and then plug it in again really hard. Then cross your fingers and hope for the best. The plugs should slide in place smoothly with minimal effort. If you feel you are applying too much pressure, something is wrong and you will bend the pins. Don’t.
  6. Put the mirror thing (32 channel/Avotec) in, there are grooves on the side and they fit the grooves of the coil. The mirror thing shouldn’t wobble too much.
    1. Sometimes it helps to screw in the two screws on the side of the mirror thing that push against the coil. If you do, screw both sides at the same time so one side doesn’t push out the other.
  7. Adjust the Avotec eyetracking camera
    1. It’s often pointed too low on the subject’s face, you can shim the front of the eyetracking camera block with some tape if necessary.
    2. Always look at the small screen for resolution. (Update, the small screen has been very flaky so can skip this if it doesn’t work.) The Avotec feed is a digitized version of the video in the small screen. Do project the Avotec feed/physio stuff on the display screen when setting up so it’s easier to see everything at once.
      1. This screen is at the scanner console. To turn it on, there’s a white power supply to the right of the console marked “Eyetracking monitor” that will need to be turned on
    3. You should be able to see eyelashes.
    4. Tape everything down when you’ve adjusted all the knobs. Everything includes: the focus of the camera lens, the camera, the IR light source, etc. The bed vibrates enough to vibrate the camera out of focus, and the whole thing will oscillate if you don’t tape the camera/IR light to the side frames.
    5. Eyetracking camera troubleshooting if there is nothing on the screen
      1. Did you turn the IR light up? It should be at 60-100%.
      2. Is the IR light cable loose? If so, wiggle it around/push it in and hope it works.
      3. Did you use the fiber optic cable marked “Use Me”?
      4. Check the mirror. There are two mirrors - an IR-transparent one and an IR-reflective one. The reflective one is used for cameras in the back of the bore and the transparent one is used for cameras in the front of the bore.
      5. If all this fails, email Rick/Ben. The connector gets worn out over time and loses optical clarity and will need to be replaced.
  8. Section on Eyelink goes here
  9. Put the squeeze ball in the subject’s armpit. This leaves their hands free to touch things.
    1. I’ve personally found armpit to be hard to use -TZ
  10. Give them the button box, do the pulse oximeter.
    1. Pulse Ox goes on ring finger of non-dominant hand (least calloused finger) with light on the palm side of the finger
  11. Put their legs on a leg cushion. Always use the leg cushion, apparently this prevents movement in the upper body when someone moves their legs.
  12. Ask them if they want a blanket. Make sure the sides of the blankets are tucked into the bed so they don’t get caught on anything.
  13. Hold the cables as you put the subject in.
  14. Give them elbow pads.
  15. Quickly switch the input screen to be from stimmy, make sure there is a lot of text on the screen so they can see if the screen is in focus.
  16. Go to the back and adjust the screen. Make sure the screen is at the second red tape position (the one closest to the projector).
  17. Check that the projection image is the right size on the screen. The bottom of the image should line up with the bottom of the physical screen. The top corners should barely be cut off.
    1. The large plastic side knobs adjust the up/down position of each side of the screen.
    2. One of the lens rings adjusts screen size.
    3. Another one of the lens rings adjusts screen focus.
  18. Make sure they are ok! Then tell them you’re talking to them from the outside.

While scanning

  1. Ask subject to test the squeezeball through the speaker.
  2. Tell the subject that you are setting things up
  3. Preferred way to communicate is to type text at them and have them respond using the button box
    1. This minimizes movement
    2. 1 for yes/ok, 2 for no, 3/4 for “I need to talk”
  4. Do all the patient registration stuff.
  5. Do localizer scan.
  6. Do quick slice and tell subject to keep eyes open so you can do eyetracking at the same time.
  7. Everything else as usual.
  8. The Goal is to be able to check through slices while the subject is doing their fieldmap for every run.
  9. Be sure to note things like level of IR (in %) for eyetracking at the top, whether the subject took breaks in the middle, and comment on ghosts in the notes for each run. Also movement (which TRs) and subject alertness of course.
  10. Do eyetracking calibration at the end.
    1. Start eyetracking on stimmy and then turn off physio to avoid collecting the eyetracking TTL pulse.
    2. Then once eyetracking has started up smoothly, start sending data over. :(

Localizer Scanning Protocol

(From Fatma's Localizer Scanning Document)

  1. Register subject
    1. Patientname: SS
    2. GALLANT / Head First Supine
  2. Scanning 1. We don't use the laser anymore 2. Start BIPOAC 3. Start Eye tracking 4. Test Squeeze Button. Ready?
    1. Run 0 (Head-case anatomical with the 12-channel, 8:45 min)
      • SHARED/Anatomical/localizer
      • SHARED/Anatomical/highres-T1-anatomical_BIGFOV (APPLY)
    2. Anatomical localizer
      • SHARED/Anatomical/localizer
    3. Quick slice positioning
      • SHARED/Anatomical/quick_slicepos
    4. EPI scans
      • Start time:
      • Stop time:
      1. Run 1 (Auditory localizer, 10:40min)
        1. Try to run this when you do sound as well.)
        • Call: python stimuli/localizer/auditory/playSound-localizer.py
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_AuditoryLoc (APPLY)
      2. Eye tracking calibration (python stimuli/eyetracker/play.py)
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • eyetrackercalib_standard_shim (BOLD 1 TR only to get the trigger!) (APPLY)
        • Stop ACQ. Software / Save file under RUN / Restart for the next run
      3. Run 2 (Category localizer, 4:10 min, play.py sessionnr runnr)
        • Task: (i) Fixate, (ii) one back task if the same image is shown twice in a row, press a button
        • Call: python stimuli/localizer/categories/play.py 1 1
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_CategoryLoc (APPLY)
      4. Run 3 (Retinotopy, 8:56 min, python play.py session_index)
        • Task: Fixation
        • Call: python stimuli/localizer/KathleenRetinotopy/play.py w1
        • COPY FIELD MAP PARAMETERS on FIELD MAP
          • Click Adjust Volume and a APPLY to the EPIs!
          • (This allows the slice selection to be in the same shim volume as previously.)
        • SHARED/retinotopy/ep2d_ret_TE30ms (APPLY)
      5. Run 4 (Category localizer, 4:10 min, play.py sessionnr runnr)
        • Task: (i) Fixate, (ii) one back task if the same image is shown twice in a row, press a button
        • Call: python stimuli/localizer/categories/play.py 1 2
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_CategoryLoc (APPLY)
      6. Run 5 (MT localizer, 5:21 min, python play.py)
        • Task: (i) Fixate, (ii) press a button when the fixation turns yellow
        • Call: python stimuli/localizer/mt/play.py
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_MTnew (APPLY)
      7. Run 6 (Category localizer, 4:10min, play.py sessionnr runnr)
        • Task: (i) Fixate, (ii) one back task if the same image is shown twice in a row, press a button
        • Call: python stimuli/localizer/categories/play.py 1 3
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • ep2d_neuro_Base20120312_CategoryLoc (APPLY)
      8. Run 7 (Retinotopy, 8:56 min, python play.py session_index)
        • Task: Fixation
        • Call: python stimuli/localizer/KathleenRetinotopy/play.py w2
        • COPY FIELD MAP PARAMETERS from earlier Retinotopy
          • Select “With Center of Slice Groups...”
          • Copy Parameter again and a APPLY to the EPIs!
        • SHARED/retinotopy/ep2d_ret_TE30ms (APPLY)
      9. Run 8 (Category localizer, 4:10min, play.py sessionnr runnr)
        • Task: (i) Fixate, (ii) one back task if the same image is shown twice in a row, press a button
        • Call: python stimuli/localizer/categories/play.py 2 1
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • ep2d_neuro_Base20120312_CategoryLoc (APPLY)
      10. Run 9 (MT localizer, 5:21min, python play.py)
        • Task: (i) Fixate, (ii) press a button when the fixation turns yellow
        • Call: python stimuli/localizer/mt/play.py
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_MTnew (APPLY)
      11. Run 10 (TOM localizer, 5:09min)
        • Task: (i) Read, (ii) Answer Yes or No
        • Call: python stimuli/localizer/tom_text/movieselect.py 2
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_TOM (APPLY)
      12. Run 11 (Category localizer, 4:10min, play.py sessionnr runnr)
        • Task: (i) Fixate, (ii) one back task if the same image is shown twice in a row, press a button
        • Call: python stimuli/localizer/categories/play.py 2 2
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • ep2d_neuro_Base20120312_CategoryLoc (APPLY)
      13. Run 12 (Retinotopy, 8:56min, python play.py session_index)
        • Task: Fixation
        • Call: python stimuli/localizer/KathleenRetinotopy/play.py r1
        • COPY FIELD MAP PARAMETERS from earlier Retinotopy
          • Select “With Center of Slice Groups...”
          • Copy Parameter again and a APPLY to the EPIs!
        • SHARED/retinotopy/ep2d_ret_TE30ms (APPLY)
      14. Run 13 (Category localizer, 4:10min, play.py sessionnr runnr)
        • Task: (i) Fixate, (ii) one back task if the same image is shown twice in a row, press a button
        • Call: python stimuli/localizer/categories/play.py 2 3
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • ep2d_neuro_Base20120312_CategoryLoc (APPLY)
      15. Run 14 (Motor localizer, 11min)

        • Tasks: Always fixate,

          • (1) hand: drumming motions with all your fingers together, without moving your wrist and arms, do that continuously as long as you see the word “mouth” on the screen
          • (2) mouth: move your mouth as if you were saying bala-bala-bala, without actually voicing it, try not to move your jaw, keep the movement small, do that continuously
          • (3) foot: drumming motion with all your toes together without moving your ankles or legs, keep the movement small, do that continuously as long as you see the word “foot” on the screen
          • (4) speak: In your head talk about what you did today as long as you see the word “speak” on the screen (no voicing, no lip movements)
          • (5) saccade: No thing that says saccade, only a pattern of dots. Move your eyes, look at the different dots, look around the dots the whole time the screen is visibl
          • (6) Rest: Do nothing, only fixate on the dot

        • Call: python stimuli/localizer/motor/play.py

        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!

        • SHARED/localizers/ep2d_neuro_Base20120312_MotorMixedLoc (APPLY)

      16. Run 15 (Retinotopy, 8:56min, python play.py session_index)
        • Task: Fixation
        • Call: python stimuli/localizer/KathleenRetinotopy/play.py r2
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS from earlier Retinotopy
          • Select “With Center of Slice Groups...”
          • Copy Parameter again and a APPLY to the EPIs!
        • SHARED/retinotopy/ep2d_ret_TE30ms (APPLY)
      17. Run 16 (TOM localizer, 5:09min)
        • Task: (i) Read, (ii) Answer Yes or No
        • Call: python stimuli/localizer/tom_text/movieselect.py 2
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_TOM (APPLY)
      18. Run 17 (AV-SNR, 2:39 min x 5 )
        • Call: python stimuli/avsnr_120/mplayer_wrapper.py avsnr150s_24fpsHD.mp4
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_AVreps (APPLY)
      19. Run 18 (AV-SNR, 2:39 min x 5)
        • Call: python stimuli/avsnr_120/mplayer_wrapper.py avsnr150s_24fpsHD.mp4
        • Re-shimm: Options → Adjustments → (Show) → Invalidate All
        • gre_field_mapping (and shimming => 3min)
        • COPY FIELD MAP PARAMETERS on FIELD MAP and a APPLY to the EPIs!
        • SHARED/localizers/ep2d_neuro_Base20120312_AVreps (APPLY)

Settings:

Biopac Settings should be as below:

Biopac Settings