MEG Acquisition

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Always make sure you have tested the entire experiment for triggers, button responses etc., once before scan subjects and collect data. When you are ready with your experiment, you can start data acquisition. Please contact the Candida Ustine the MEG Engineer to schedule a time for your data acquisition. Make sure that either the Engineer or an MEG experienced researcher is present at the MEG suite when you are scanning. There must be atleast one person from your research group who is familiar with the MEG scanning procedure, present for the entire scan time that is scheduled for you. You will be helped by the MEG engineer or the Technical Manager if you need assistance. Make sure to have additional help if you are doing an simultaneous EEG acquisition for help with the cap setup. See the section on Training if you like to be MEG trained.

Starting the Acquisition Program

In the Neuromag folder, open the Acquisition program. Load your project and settings; details on how to use the program are below in the Data Acquisition These settings should have been previously created and saved so that time is not wasted while the subject is present. Once the necessary settings are loaded and double-checked, you are ready to register the subject.

Subject Registration

With the HIPAA regulations we have made several changes in how to register subjects, so be sure to follow these steps in order to be compliant! Press the “Change” button next to Subject: Enter name, birth date, sex, and handedness (height/weight can be skipped)


Once registration is complete, you are ready to digitize the subject. Turn on the Polhemus system, which is used for digitization, and is located on the table in the patient prep area. Instructions for using the system are as follows:

  • Move the wooden chair away from the Polhemus system.
  • Have the subject sit in the wooden chair
  • Move all rolling chairs and other objects with large metal components away from the chair and Polhemus
  • Position the goggles on the subject’s head, being careful not to cover up any electrodes or HPIs. It is critical that the goggles are tight and do not move once digitization has begun.
  • In the Acquisition program on megacq1, press the “Change” button next to HPI. At this point you will be prompted to digitize cardinal landmarks, HPI coils, electrodes, and extra head points. At the top of the screen, hit the “Coordinate frame alignment” button; you are now ready to begin digitization
  • Digitize the three cardinal landmarks (left pre-auricular point, nasion, right pre-auricular point, see below) by pointing to each and simultaneously clicking the button on the stylus.
  • It is a good idea to check that the two ear points are within a maximum (absolute value) distance of 5mm.
  • After the third point has been digitized, you will hear two beeps instead of one—this is simply to indicate that you are done digitizing a section. If at any point during the digitization of the different sections you hear two beeps (before the last point), you have accidentally pushed the stylus button twice and should start over.
  • Instructions on how to do this are Data Acquisition further below.
  • To move on to the next section (HPI coils), there is no need to click anything else; you will simply be prompted to begin digitizing HPI.
  • Digitize the four HPI coils in any order. Be very careful when digitizing these points, as they can come back to haunt you later if not done properly the first time!
  • Next, if using the EEG cap, digitize the electrodes in order, starting with the reference electrode. A map of electrode locations can be found on the bullaten board next to the Polhemus.
  • If not using the cap, you will not be prompted to digitize any electrodes (unless you failed to rename any of your facial electrodes as EOG rather than EEG).
  • Finally, you will be asked to digitize additional head points. It is a good idea to make a straight line down the forehead and nose, as the nose is easily identifiable in the subject’s MRI. An extra 50 or more points from the head should be taken so to cover the head; these will also be used in conjunction with the MRI.
  • When finished, hold the stylus about a meter away from the subject and press the button.
  • If at any point you should make a mistake, you can hold the stylus away, press the stylus button, and then click on the button at the top of the section you would like to do again. This will clear any points taken in a given field, allowing you to start over. (It will not clear points in previous fields).

Connecting HPI, EEG Electrodes to Vectorview

The plug for the HPI coils is inserted into the "subject’s" right side of Vectorview. The plug has a small notch on it; this should be placed downwards, and the whole plug should be positioned so that extra spaces are on the right. The earphones are also plugged in on the subject’s right into the slot labeled “auditory stim out.”

All electrodes are plugged in on the subject’s left. For EOG and other bipolar electrodes, be sure to pair them together correctly (e.g., vertical with vertical and not vertical with horizontal), although which goes in (+) and which goes in (-) is unimportant. Ground and reference are plugged into the same location labeled ground and reference, respectively. If using the EEG cap, the cap’s connectors should be plugged into the slots with corresponding numbers.

If doing an auditory study, be sure to place the earphones in the subject’s ears before raising the subject up into the helmet. The foam insulation for the earphones can be found in the cabinet above the analysis workstation. To adjust volume, use the audio adjustment in the stimulus PC.

If any of the supplies are running low please contact Candida Ustine about it. It is a Froedtert Facility.

Placing Subject in the Helmet

The pump for the chair is located on the [subject’s] right; the longer lever pushes the chair up; the shorter one lowers it. Subjects should be pushed up far enough so that they can feel pressure on the top and back of their head. It is important to have the subject first slouch down and get comfortable so that they do not do so later and slip down in the helmet. If using the bed, lock the wheels and move only the upper portion of the bed. This way subjects can position themselves comfortably, and you can easily slide them into the helmet until their head touches the back.

Subject Instructions

Before exiting the MSR, be sure to remind the patient of both the general MEG instructions as well as any instructions specific to your task. General instructions include:

  • For auditory studies, focus on a point on the wall or a fixation cross displayed on the screen; for visual studies, focus on the fixation cross.
  • For any kind of stimulus, try not to blink while stimuli are being presented or while responding.
  • Do not move once the measurement has begun.
  • To communicate with the experimenter, simply speak aloud; there is a microphone built into the machine. However, you should avoid speaking during a measurement, unless it is an emergency.
  • Be aware that there is a camera in the room and that we can see you from outside.

Data Acquisition

See Scanning_Specifics Page for information on setting your scanning parameters and for info on troubleshooting. For a detailed description of the acquisition software and how to create your acquisition settings, see the Vectorview manual, section five (this manual can be found online as well as in the MEG lab. Neuromag Manuals page

Entering Task and Subject Info

  • Log into the MEG Acqusition System. Contact the MEG Engineer for Login Information.
  • Select Neuromag Folder --> Acquisition
  • The Settings Dialog Box opens
    • Change: Project
    • Change: Subject
    • Change: Acquisition
    • Change: Stimulus Generation
    • Change: Online averaging
    • Change: HPI
  • Select a Project from the list
  • Go to File --> Load Settings. (You will find a list of saved projects/studies in your user directory. Select the appropriate study and all the settings will be automatically loaded) (NOTE: If you are setting your experiment for the first time then visit the Scanning Specifics page to read information/suggestions on choosing scanning parameters.
  • Subject Registration: You should never enter patient identifying information here(NAME)!! See Subject Registration above for more information.

Beginning a Measurement

Below the six “Settings” buttons is a series of buttons marked “Acquisition Controls,” which read from left to right: GO, Stimulate, Average, Record Raw, Restart, and Stop. Hitting GO will start acquisition. (It may be up to ~10 seconds before you see any channel activity, so be patient!) Once the channels come up, it will take several more seconds for them to settle; you can shorten this process by going to “Tools” and “Reset Channels.”

Initial Check

Before beginning stimulation and recording any data, briefly browse through all channels to make sure that none are showing artifact. To do this, click “Selection” at the bottom of the raw display window (which automatically popped up on the right monitor when you started the Acquisition program). You will then see a list of channels, grouped both by location or number; either is suitable for looking at the channels. Go through each section to check the channels one by one.


If you do find any sensor showing some artifact, you can usually perform a quick fix by heating the sensors. See my page on Sensor Troubleshooting and follow the directions.

Measuring HPI

Once all channels look fine, you are ready to measure the subject’s head position. A window prompting you to do this will have automatically popped up after hitting GO. In this window hit the “Measure” button, and wait several seconds until a new window with the HPI results pops up.

If everything went well, the suggestion at the bottom of the window will say “Accept.” After accepting, you are ready to begin recording.

When HPI is not OK

Occasionally you will find that one out of the four HPIs is not OK, yet the suggestion is still “Accept.” This is true because the system only requires three functioning HPIs; however, having all four function properly is preferred in the event that one fails, in which case you will still receive the “Accept” suggestion and be able to move ahead.

If less than three HPIs are OK, the suggestion will be to “Redo HPI.” In the event that you receive the Redo message, re-measure the HPI and see if things improve. If not, scan through all channels and tune/reheat any that are noisy. A noisy channel can compromise the HPI measurement. Ask also the subject to help his breath for a few seconds while HPI measurement is running (breathing artifacts w/ VNS may impede measures). Try measuring again.

If the suggestion is still “Redo HPI”, you may need to remove the subject from the MSR and see if one or more of the HPIs have come loose. If yes, redigitize subject and start over.

Data Recording

At this point you should have your stimuli ready to present to the subject. Before beginning presentation, however, be sure to hit the “Record Raw” button first for all recordings and then the “Average” button for evoked recordings; this will ensure that all trials are included in data collection.

As stimuli are presented and the subject responds, you will see a list of trials (or “epochs”) collected for each different category designated in the online-averaging setup. If a trial is excluded from the average, a message indicating why is displayed at the top of the Acquisition window. Most often trials are rejected due to eye blinks, which would show as EOG 61 or 62. If an MEG channel is frequently causing rejections, attempt to heat or fix otherwise before beginning the next run. (However, never heat a channel while actually recording data).

If you feel that the subject is blinking too much and you want to restart the run, de-select the Average and Record Raw buttons, and hit “Restart.” This will clear all data collected and allow you to speak with the subject, re-measure HPI, and begin recording again.

When the run is over, hit STOP and save your data (details on saving are below). Most likely you will be collecting several runs, so after saving your data, simply hit GO again and follow the above steps.

Saving your RAW Data

Saving Data At the end of a measurement, hitting “Stop” in the acquisition window will automatically bring up a window prompting you to save your data—first evoked and then raw data (if both were collected). Data is saved directly to a raid rather than the local disk.

Simply name your file with the extension "_raw.fif" and hit save.

Subject Exclusion Criteria

Subjects who are ready to be run on the MEG machine must satisfy the following criteria

  • Weight
  • Height

After Data Acquisition

After you have collected data the raw data is saved in the MEG suite computer . You will have to transfer the data to your own workstation that might probably not be in Froedtert. In this case please contact the MEG Engineer Candida Ustine in order to transfer yoru raw data. Please see Data Transfer for more information.