L9: MEG Preprocessing Flashcards
Preprocessing of MEG data involves - (3)
- Inspecting MEG data
- Epoching
- Dealing with noise (e.g., noise reduction, noise removal [filtering, automatically/manually rejecting noise trails], averaging)
Preprocessing and event-related analyses of MEG is similar to
EEG (apply similar steps)
What is MEG data measuring for each sensor?
magnetic field strength over time
An MEG system samples from lots of
sensors at lots of points in time
What is the typical sampling rate for MEG per second and millisecond - (2)
around 1000 Hz (1000 samples per second)
1 sample per millisecond
Why does MEG have a sampling rate?
MEG has amazing temporal resolution (when the activity has happened) so don’t need MEG’s data everytime time
Our MEG system in York has around how much sensors?
248
The EGG in York has approximately how many electrodes?
64 and 128 electordes
The raw data from MEG can be stored in a very large
Time x Sesnor matrix
What is shown in the rows and columns?
Along the top is the different sensors in MEG and along the bottom is millisecond
MEG’s Time x Sensor matrix in a 10-minute worth of data can have how many rows and columns with 248 sensors
600,000 rows and 248 columns
MEG’s Time x Sensor matrix , each entry in the matrix is
the magnetic field strength detected by a given sensor at that point in time, measured in femto-tesla (10 to the power -15 telsa)
In EEG, we can have a matrix of electrode x time in which each entry
EEG values which are the magnitude of the electrical (activity) potential in microVolts
MEG’s timecourse for all sensors can initally be
inspected
First step of MEG - inspecting MEG data across time
Diagram of MEG time course for all sensors which plots.. and what are y and x axis - (2)
plots the timecourse for all the sensors
y is the magnetic field strength (femto telsa [fT) and x axis is time in seconds (s)
First step of MEG- inspecting MEG data across time
What can you see in this example? - (2)
6 sensors are very noisy (noisy lines underneath - broken sensors which should be removed)
others sensors are more stable showing a gradual drift (cone) of some picking up stronger magnetic field strength and others not so much –> some sort of artefact (e.g., changes in temperature/changes in magnetic noise)
Although inspecting MEG data across time is not usually informative, it can reveal
gross problems such as dead sensors or big artefacts
Inspecting MEG data such as one below is not enough to answer
our RQ
Usually in MEG studies, we would want to present stimuli at specific times and see how the brain responds
this is like what design in MRI?
event-related design
What does this diagram show? - (4)
- Participant and their EEG/MEG recordings are being taken
- Pps is looking at dog at stimulus PC
- Then the stimulus PC sends a trigger (i.e., i showed image of puppy at this time) to EEG/MEG recording PC
- Then EEG/MEG recording PC adds this to the data as the little 1s demonstrate when participants saw the puppy
- This way know exactly when pps were shown something and look at the brain activity after they have done that to see when we show them a puppy
Different conditions have triggers with different
numbers
Diagram of example of different conditions have triggers with different numbers - (2)
- Aside from recording when participant saw a puppy in MEG trace (e.g., 1)
- We can also record when participants saw a cat (another condition) in MEG trace which is 2
What is a trigger in MEG?
A trigger is indicating stimulus onset is stored as a number in MEG
Typically, the stimulus presentation PC sends the trigger signal to the
EEG/MEG recording PC
In epoching, we can extract an ‘epoch’ of data around the
stimulus time [onset] (around trigger)
In epoching, we want some time before… and after… (2)
time (e.g., 500ms) before stimulus presentation as baseline and enough time after to see effects (e.g., 1500ms)
Why do we epoch some data (e.g., 500 ms) before stimulus presentation? - (2)
- The effects we may see after stimulus presentation may be due to activity already going on in brain - lots of spontaneous activity
- Acts as baseline and expect change to happen after that 500 ms
Diagram of epoching shows… (3)
- Showed 100 puppies
- After each time we showed them puppies (1s), we can look at the data after a 1 second or so and epoch it
- This image does not include any baseline
In epoching we can extract the data before and after stimulus time (around trigger) in each.. - (2)
each trial in one condition
(e.g., epoch data for when pps seeing dog, epoch data when pps see cat)
In epoching, we can also have trial by trial
data
What does this trial of epoching of trial by trial data time course plot show? - (7)
- 0 timepoint which is the stimulus presentation
- baseline before 0
- 0.5 and 1.0s (after 0) after stimulus presentation
- Red is positive and blue is negative
- Have different sensors at different trials
- At 0.6s all sensors are consistently showing some change when showing some stimulus (e.g., puppy)
- By looking at individual trials start to see effects consistent across sensors or across different trials (e.g., look at next trial showing puppy to see if we also have something [effect] at 0.6s)
In epcohing trial by trial data we can view data at one trial across
different sensors
In epoching trial by trial data, external noise such as… can often show up as …
subject movement and other artefacs (as well as real effects) often show up as correlated activity across sensors
In epoching trial by trial data the timings are now meaningful as 0
is stimulus presentation, see what changes
What is this diagram - (2)
This is a sensor montage which plots epoching trial by trial data in a different way (as compared to timeplot)
- plots amplitude across different sensors in montage of head
It is very hard to distinguish EEG/MEG signal from
noise
The noisiness in EEG/MEG signals tend to be - (2)
much bigger than effects we are looking for (tiny magnetic strength/electrical potential effects)
problem for preprocessing EEG/MEG data
What does this diagram show? - (2)
brain’s magnetic fields we are looking for in an experiment are very small (down)
above it we have sources of magnetic effect that can reduce ability to see small experimental magnetic effects (e.g., earth’s magnetism, magnetic noise of town)
What are many noise sources in MEG (and EEG)? - (3)
- electromagnetic interference from cars, mains power line, fans, MRI scanners etc..
- Earth’s magnetic field
- Participant movement, blinks and own heartbeats
Blinks of a participant show up on a
Electrooculography (EOG)
To detect and remove the blink artefacts in EEG/MEG
we use
electroculogram (EOG) sensors)
What does EOG stand for?
Electrooculography
EOG sensors is the
additional electordes placed on face to monitor blinks and eye movements
EOG may lead to
positive and negative voltage changes at some scalp electrodes
What does this diagram show? - (2)
Recordings of EOG is shown at the bottom two traces (circle)
These traces causes massive electrical /magnetic changes in EEG/MEG data when participant blinks
What does this diagram show in EEG? - (3)
- The eye movements and blink have a specific topography sensors
- Has effect where positive charge at the front of head and negative at back
- If we see this kind of activity, we may see this as a blink
Can also use ECG sensors with EEG/MEG which record
electrical activity of the heart including rate and rhythm
What does ECG stand for?
electrocardiogram
Can also use ECG with EEG/MEG to remove heartbeat effects but less likely to - (2)
be correlated with task/stimuli presentation
(good thing! = enables us to do comparisons properly without worrying about heartbeat correlated unless comparing older vs younger which have different heartbeat rates)
What are common artefacts in MEG? - (3)
- Blinking
- Eye movements
- Heartbeat
Diagram of blinking in sensor space vs source space in MEG
What is this diagram showing of 3 different artefacts in MEG and why is its topgraphy of sensor space (eye movements) different to EEG? - (2)
We have different topography of different magnetic effects across MEG sensors when we blink, move eyes to the right and the heartbeat
This topography is different as whenever you have an electric charge you get a magnetic field that is perpendicular to it
The problem of noise (artefacts) is that it causes us to
not ‘see’ neural signals on a single trial
sa
We can deal with noise in the data by doing 3 things - (3)
- Noise reduction
- Noise removal (filtering, automatically/manually rejecting noisy trials
- Averaging
What is the solutions with noise reduction when doing the experiment? - (3)
- study design should minimise movement, including eye movement and identify movement between conditions (i.e., no movement expected in one condition than another, get pp comfortable in scanner and get cushion and blanket)
- Experiment taken place in magnetically shielded room (Faraday cage) –> earth’s magnetic field effect will reduce, no electrical machinery in scanner, de-mental the partticipants
- Automatic comparison to reference channels
Reference channels in MEG systems is where their coils are positioned far away from
participants’ head
The purpose of reference channels is that
real MEGs sensors can be compared to the reference channels
Diagram of what inside of MEG scan looks like and what it shows… - (3)
SQUIDs stay cold so near liquid helium reservoir
Pink is signal coils picking up the magnetic signal and trying to send it near to SQUID
In between wehave green reference sensors which does not pick real brain activity but nearby to pick ambient things (e.g., traffic, earth’s magnestism
The reference electrodes are intended to pick up
ambient noise and interference not coming from the participant
The reference signals are then subtracted from the
real signals from rest of real MEG sensors = taking a lot of external sources of noise
How is subtraction of reference signals from real signals from MEG sensors is done? - (2)
done automatically (see ‘processed’ vs ‘raw’ folders)
OR
MaxFilter software for signal space separation has similar aim based on decomposing data to tell which are probably far from head
Noise reduction from reference electrodes does not help in detecting and removing
noise from the participant - reference electrode too far from the participant