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The content for troubleshooting should be organized under each of the top-level categories. This page is just a quick way to get to each of those. E.g.:




Be aware of whether your protocol is run in normal mode or first level. You must make a choice in the pop-up window after you have chosen your protocol but before you can actually start scanning with your protocol. If your protocol has been set up to be run in First Level and you choose Normal Mode, you will see an advisory error window pop-up. The machine adjusts parameters in order for the sequence to run the alternative mode and sends an advisory message.


The GE Screen over the scanner bed can display three views: the standard GE views, the eye tracking interface, and the CNI computer.

  1. If you would like to change the view that is being displayed, find the box (brown color) which sits on the large GE computer next to the GE console monitor (FORP box and scan trigger box are close by).
  2. Locate the three possible displays labelled on the top of the box.
  3. Push the button for the one that you would like to have displayed on the screen.


If you are having a problem with the High Order Shims (HOS) i.e. the shim values are not downloading, bring over a fresh copy the HOS sequence from your protocol and rerun the sequence. If that does not solve the problem, the system may have to be rebooted. See CNI staff or go to the rebooting (restart) section in the troubleshooting area.


Make sure that the table is all the way out of the bore of the magnet.

  1. If the "Home" button light is lit, then the table is not all the way out. If you try to landmark a participant with table in this position, the scanner may or may not recognize your new landmark.
  2. Push the "Table Out" to move the table all the way out. You will hear a "clunk" sound when the table reaches its home destination.
  3. When this is done you can then landmark the participant.


The length of EPI fMRI sequences can be adjusted in the second "Multiphase" tab in the sequence parameter window area. The parameter in this tab "Phases per location" (number of frames) will change the length of the sequence. Type in a number, hit the return button and the time duration of the sequence will be updated. The maximum value is 512. With this value the sequence will run about 17 minutes.


Always check to see that your participant can see visual stimulus on the screen.


1. Hook up your computer to the cable labeled "Goggles".
2. Set the monitor display to "right".
3. Set your screen display to 800 x600 (make sure your stimulus program does not change the screen resolution).
4. Check that the subject can see the screen through the goggles.
5. To position the goggles on the subject head when scanning with the 32 channel coil you need to close the coil first and the slides the googles either from above or below.
Please note that the goggles have a rubber casing to position on the subject's face. Don't dismantle.


To restart the scanner first locate the "Tools" icon at the upper left hand corner top of the screen. It is in the trio of icons along with the Patient entry and Viewer icons. The "Tools" icon has a drop down menu. "System restart" is one of the entries on the drop down menu list. Click on "system restart" and the system will reboot itself in the next 5-10 minutes. The process will automatically type in the password. In the process of boot-up, a window will appear indicating not to interact with the system until this particular window has disappeared from view. When that occurs the system is ready to use.


In the "Advanced" tab of the fMRI (BOLD EPI) there is a "Start Scan Trigger" parameter. The value can be either 0 or 1. If the value is 0 the scanner will start scanning when the "Scan" button is clicked. If the value is 1 the scanner will start scanning when the "Scan" button is clicked only if an external trigger is received from your stimulus.


There are two voice volume controls on the GE keyboard. The right hand volume control controls the volume of sound coming from the scanner room. In order to better hear anything your participant has to say, turn up the volume while communicating with the participant. After you start to scan you should turn the volume down to minimize the volume of the scanner.



  1. Make sure the audio cable is plugged into your computer. [PICTURE]
  2. Make sure your computer's audio is turned on and set to an appropriate volume level (85% tends to work well). [PICTURE]
  3. Make sure that the Visuastim sound system is turned on and set to an appropriate volume (check 'Patient Volume'). [PICTURE]
    1. Use the white controller on the scanner console desk and enter the menu. Check that Audio is turned ON. [PICTURE]
  4. If the audio is still not working, try this:
    1. Turn the Visuastim box on and off. Then play your sound again. Note that the first time you play the sound, it may be very faint/quiet. If this is the case, stop playing the sound, and then start playing it again. The second time around it should be at the set volume.
    2. If turning the Visuastim box on and off did not fix the problem go to the equipment room and turn the black power supply that the stimulus equipment is connected to off and then on again. [PICTURE]


If the biopac isn't working, go to the equipment room, unplug the system from the power supply, and plug it back in. [PICTURE]

Read more details about the Biopac and other physio monitoring here: MR_Hardware#Physio_monitoring.


  1. Make sure that you have plugged in the button box that you intend to use and that the fiberoptic connection is good (it might take some adjusting for the button box cable to be plugged in properly).
  2. Make sure that you have the fORP box [PICTURE] on the correct setting. They are:
    1. 4-button cylinder [PICTURE]: HHSC-cyl-5
    2. 5-button diamond [PICTURE]: HHSC-1x5-D
    3. 5-button curved [PICTURE]: HHSC-1x5-C
    4. bi-manual 4-button keypads [PICTURE]: HHSC-2x4c
    5. scrollwheel [PICTURE]: HHSC-SCRL1
    6. trackball [PICTURE]: HHSC-TRK-2
    7. bi-manual button hands [PICTURE]: connected to computer via USB and shows up as keyboard.
  3. If all connections and settings are correct, power-cycle the fORP box. [PICTURE]

Read more details about the response boxes and how to set them up here: MR_Hardware#fORP_Response_Box.


  1. If the E-prime program is not opening the correct device, open the ES file of your program in E-studio to check device connectivity. To do so, double-click on the Experiment object at the top of the Structure window and navigate to the Devices tab. Then double click on 'Serial' to change the address of the port to match your available serial port. The USB port (SRBox) is set to COM3, so make sure the serial port matches (you can also verify the port number that your SRBox is using via the Windows Device Manager).


  1. This screen will only display your laptop screen if they are set to the same resolution; otherwise the flat panel display in the control will appear black and give an out of range error.


  1. Make sure that the screen is turned on. [PICTURE]
    1. If the power button on the screen does not seem to be working, go to the equipment room, and turn the black power supply off and then on again. [PICTURE]
  2. If the screen is turned on, but is flashing in various colors, go to the equipment room, and turn the black power supply off and then on again. Note that this will only work if you disconnect your computer from the LCD screen connector while you do the power-cycling. [PICTURE]
  3. If the screen is turned on, but the colors are not displayed correctly, make sure that the connector cable is plugged in properly into your computer. [PICTURE]
    1. If the connector cable is plugged in properly, and there is no loose connection, make sure that the connector is intact (e.g., no bent or broken pins, etc.). [PICTURE]
      1. If the connector appears to be broken, contact the CNI staff.
  4. Make sure that your computer screen is set to the correct resolution. The LCD screen in the scanner room has a resolution of 2560x1600, 7ms temporal response, and 10-bit color rendering.

Read more details about the LCD screen and how to set it up here: MR_Hardware#Flat_Panel.


  1. To start the video recording, open the command window on the scanner console. You will run the 'recordSubject' script and specify the recording duration.
    1. For detailed instructions on how to record video or display it on the big screen in the control room, consult this page: MR_Hardware#Physio_monitoring.



  1. If the participant has trouble reading or seeing your stimuli, he or she might need glasses.
    1. Check their vision using the vision chart in the control room. [PICTURE]
      1. Outfit them with MR-safe glasses.
        1. If they have glasses, you can determine their prescription by measuring their glasses using the lensometer. Learn here how to do so: MR_Hardware#Lensometer.
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