Independent Component Analysis (ICA)

In the context of EEG, MEG and applications in other modalities

Sriranga Kashyap
I6046171

Course: PSY4256 - Timing Neural Processing with EEG and MEG

We can complain because rose bushes have thorns or rejoice because thorn bushes have roses - Abraham Lincoln

Abstract
The phenomenal advancements in technology in the past decade have made it possible to study non-invasively, various hitherto unthinkable, properties of the living human brain. This results in a lot of data and thus, important to extract the essential features from this data to allow interpretation of its properties. Traditional approaches to solve this feature extraction include principal component analysis (PCA) and factor analysis (FA). This paper focuses on using a novel data-driven method, independent component analysis (ICA) that allows blind separation of sources by assuming their statistical independence. The first part of the paper reviews ICA and compares ICA with PCA and FA (non-technically). The next part addresses ICA in the context of vintage imaging methods such as EEG and MEG, its role in source separation and artefact rejection. The final part emphasizes the versatility of ICA by describing applications to functional imaging, combined modalities and discusses a recent application to source characterization. Keywords independent component analysis, artefact, source separation, EEG, MEG

Table of Contents Abstract ....................................................................................................................................... i 1 Introduction ........................................................................................................................ 1 1.1 1.2 2 Overview ..................................................................................................................... 1 ICA vs. PCA and FA ................................................................................................... 1

ICA applied to the neural cocktail party (Brown et al., 2001) ........................................ 2 2.1 In the context of EEG .................................................................................................. 2 Artefact Rejection ................................................................................................ 2 Artefact Rejection: ICA vs. conventional statistical/spectral analyses ................ 2 ICA Assumptions in context of EEG ................................................................... 3

2.1.1 2.1.2 2.1.3 2.2

In the context of MEG ................................................................................................. 4 Artefact Rejection ................................................................................................ 4 Artefact Rejection: ICA-based ............................................................................. 4

2.2.1 2.2.2 3

Applications in other modalities ........................................................................................ 6 3.1 3.2 Application to fMRI data ............................................................................................ 6 Application to concurrent EEG-fMRI data ................................................................. 7 Application to EEG-fMRI at 9.4T ....................................................................... 7

3.2.1 3.3 3.4

Application to fNIRS .................................................................................................. 7 Application to source characterization ........................................................................ 8

Concluding Remark ................................................................................................................... 8 References ................................................................................................................................ iii

Table of Figures Figure 1. Cocktail Party Problem............................................................................................... 1 Figure 2. Sources of ERP ........................................................................................................... 2 Figure 3. Artefact detection performance with the five methods (columns) applied to five types of simulated artefacts (rows). Black traces: applied optimally to the best single-channel data for each artefact type. Grey traces: applied to the best single independent components computed from the data by Infomax ICA (Delorme et al., 2007)................................................................................................ 3 Figure 4. Sample of MEG signals showing artefacts produced by blinking, saccades, biting and cardiac cycle. For each of the 6 positions shown, the two orthogonal directions of the sensors are plotted (Vigrio et al., 2000) ..................... 5 Figure 5. Six independent components extracted from the MEG data containing several artifacts. For each component the left, back and right views of the field patterns are shown. Full lines stand for magnetic flux coming from the head, and dotted lines the flux inwards ............................................................................... 5 Figure 6. a) The need for higher order statistics, b) Comparison of GLM and spatial ICA for fMRI data, c) Spatial ICA of fMRI data (Vince D Calhoun, Liu, & Adali, 2009). .............................................................................................................. 6

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1
1.1

Introduction
Overview

A problem often incorrectly phrased is that of an overload of information especially with new technology. However, the problem in reality is that there is an overload of data and relatively small amount of useful information. Independent component analysis (ICA) is a method of extracting this useful information from the data. ICA belongs to a class of blind source separation (BSS) methods for separating raw data (signal mixtures) into components of information (source signals). The blind in blind source separation implies that the signal mixture can be separated into source signals without a priori knowledge of the nature of the source signals. ICA can be best understood with the cocktail party problem (Stone, 2002). Consider two people speaking at the same time in a room with two microphones. If each voice signal is examined on a ne time scale it is observed that the amplitude of one voice is unrelated to the amplitude of the other voice at a given point in time. The
Figure 1. Cocktail Party Problem

reason is because they are generated by two

unrelated physical processes (i.e. by two different people). Therefore, a strategy to separate the voice mixtures is to look for the unrelated time-varying signals within these mixtures. 1.2 ICA vs. PCA and FA

ICA is an improvement over conventional methods such as Principal Component Analysis (PCA) and Factor Analysis (FA). ICA identifies a set of independent source signals whereas PCA and FA nd set of signals that are uncorrelated with each other. With respect to the aforementioned example, PCA and FA would extract a new set of voice mixtures which are uncorrelated with each other but mixtures nonetheless. In contrast, ICA would extract a set of independent signals which would be a set of individual voices. ICA is an improvement because: it assumes independence (independence implies a lack of correlation but lack of correlation does not imply independence) and based on higher order statistics (whereas PCA is based on second order statistics). Therefore, the result obtained by ICA is expected to be more meaningful than the one gained by PCA.

2
2.1

ICA applied to the neural cocktail party (Brown et al., 2001)

In the context of EEG Brain-generated EEG data is understood to represent measure of the synchronous aspects of local field potentials of radially arranged pyramidal cells in the cortex. ICA identifies signals in recorded multichannel EEG data mixtures whose time courses are maximally independent of one other. The problem of source separation is an inductive inference problem. There is not enough information to deduce the solution, so one must use available information to infer the most probable solution. Therefore, it is important to realise that ICA is not a solution to the general inverse problem in EEG.
Figure 2. Sources of ERP

However, what ICA does do is estimate the relative

projection weights of the maximally independent sources and the distinct signals in the volume-conducted data, therefore, simplify the problem of source localization not necessarily solve it (Makeig, Debener, Onton, & Delorme, 2004). However, EEG data also includes nonbrain signals or artefactual signals that are linearly mixed with brain EEG source activities at the scalp electrodes. 2.1.1 Artefact Rejection ICA can efficiently separate out stereotyped artefacts such as electromyographic (EMG), electrooculographic (EOG), electrocardiographic (ECG) signals and single-channel noise produced by loose connections between electrodes and the scalp (Jung et al., 2000). Nonstereotyped artefacts are those produced by participant movements, tugs on electrode cables etc. induce several of unique scalp maps and therefore, so these are best removed from the data before ICA decomposition. 2.1.2 Artefact Rejection: ICA vs. conventional statistical/spectral analyses A quantitative comparison of 5 different statistical/spectral analysis methods available in the EEGLAB toolbox (Extreme values, Linear trends, Data improbability, Kurtosis, Spectral pattern) to detect artefacts in the data and the same procedures to the data decomposed using ICA was carried out by Delorme, Sejnowski, & Makeig, 2007. The results are presented in Figure 3. 2

Figure 3. Artefact detection performance with the five methods (columns) applied to five types of simulated artefacts (rows). Black traces: applied optimally to the best single-channel data for each artefact type. Grey traces: applied to the best single independent components computed from the data by Infomax ICA (Delorme et al., 2007).

It can be easily observed from Figure 3., that the artefact detection performance (artefacts detected minus non-detected artefacts, divided by the total number of artefacts) for artefacts less than 40dB, all the detection methods performed better when applied to the independent component data. 2.1.3 ICA Assumptions in context of EEG 1. ICA component projections are summed linearly at scalp electrodes. This assumption is fulfilled in the case of EEG recordings which is why during an ICA decomposition, the selection of a reference electrode (or re-referencing) is not very important 2. Sources are independent This assumption is more plausible than the one that brain networks are physically isolated from one another (therefore, assuming it to be possible to clearly localize the source signals) 3

"sources" of ICA components are possibly distributed brain networks and may be functionally linked.

If during the decomposition of spontaneous or event-related single-trial EEG data, an ICA component map turns out to be compatible with a possible compact generator region in cortex then it is imperative to understand that this is not because ICA had this as an objective but because a coherent signal source, independent of other sources, projected to the electrodes in this pattern

Since the time courses of artefacts and the triggering brain events are different across most trials, they will be accounted for by different independent components (Jung et al., 2000).

3. non-Gaussianity of the activity distributions This assumption is plausible for artefactual activity as they are quite sparsely active and therefore, not-Gaussian. 2.2 In the context of MEG

MEG data consists of an unknown mixture of noise, artefact and signals from unknown brain electric sources. As was the case with EEG, these sources are cortical networks that are sequentially activated to perform simple or complex tasks. However, MEG is designed to pick up very minute magnetic activity and therefore, MEG recorded source activity is not unique to the true distribution of brain sources but contains unique artefacts. This makes it challenging to remove such artefacts usual generated by electrical activity in the body and necessitates and implementation of ICA for MEG data. 2.2.1 Artefact Rejection The most commonly used artefact correction method is rejection, based on just blatantly discarding portions of MEG that coincide with artefacts. Other methods are to instruct the subject to refrain from producing the artefacts (fixate on a target to avoid eye-related artefacts or relax to avoid muscular artefacts). The effectiveness of these methods and their end result is loss of data and questionable design in studies of neurological patients or other non-cooperative subjects. 2.2.2 Artefact Rejection: ICA-based Success of ICA to EEG data suggests an application to MEG, based on the assumption that the brain activity and the artefacts are anatomically and physiologically separate processes and that their independence is reected in the statistical relation between the magnetic signals generated by these processes.

Artefact identification in MEG recordings, using ICA, has been reported by Vigrio, Srel,

Jousmki, Hmlinen, & Oja, 2000. Figure 4. shows a subset of 12 MEG signals from a total of 122, from frontal, occipital and

temporal regions. Several artefacts such as eye and muscle activity have been shown to be possible to extract using ICA and therefore,
Figure 4. Sample of MEG signals showing artefacts produced by blinking, saccades, biting and cardiac cycle. For each of the 6 positions shown, the two orthogonal directions of the sensors are plotted (Vigrio et al., 2000)

applied to the dataset.

Figure 5. shows these artefacts extracted by ICA. IC1 and IC2 are clearly muscle artefacts identifiable by their high frequency. IC3 and IC5 are characteristic of horizontal eye movements and blinks other

respectively.

Interestingly,

disturbances with weaker SNR such as heart beat and even a watch can be extracted (IC4 and IC6). Therefore, the basic assumption of ICA that the brain and artefact waveforms are independent can be veried by the known differences in Figure 5. Six independent components extracted from the MEG physiological origins of those data containing several artifacts. For each component the left, signals. In some event-related back and right views of the field patterns are shown. Full lines
stand for magnetic flux coming from the head, and dotted lines the flux inwards

designs it can be very challenging, for example, when presenting

infrequent or painful stimuli, because both the cerebral and ocular signals would be timelocked to the presented stimulus. However, the property of independence of the two signals is a measure of the similarity between the joint amplitude distribution and the product of individual signal distribution calculated along the entire signal, not only in the vicinity of the presented stimulus. Therefore, we can expect the local relation between the signals, during the stimulus presentation period, to not affect their global statistical relation.

Applications in other modalities

As we have seen earlier, ICA has proven to be a powerful and versatile data-driven approach for studying the brain. This versatility allows us to use ICA in different modalities used in neuroscience research. Another remarkable feature that enables ICA usage is, although the nature of the type of signal measured by each modality does not affect ICA, which as discussed earlier is an excellent Blind Source Separation method. 3.1 Application to fMRI data

Figure 6. a) The need for higher order statistics, b) Comparison of GLM and spatial ICA for fMRI data, c) Spatial ICA of fMRI data (Vince D Calhoun, Liu, & Adali, 2009).

Figure 6a. shows that principle component analysis (PCA) finds orthogonal directions which explain the maximum variance (second order) whereas ICA identifies maximally independent directions utilising higher order statistics. In Figure 6b. we can see a comparison of GLM (the conventional method) with ICA, where the spatial ICA identifies temporally coherent, systematically non-overlapping brain regions without requiring a modelled temporal response. Figure 6c. illustrates the application of ICA to the fMRI data, which is assumed to be a composed of linearly mixed sources, which are then extracted along with their respective time courses. The strength of ICA in fMRI is its ability to reveal temporal dynamics even when a model is not available. 6

3.2

Application to concurrent EEG-fMRI data

The 21st century has seen exponential improvements in technology that have enabled collection of multiple types of imaging data from participants and it has become popular to do so, simultaneously using two different modalities providing information in two separate domains. For instance, EEG informs us more efficiently on a temporal domain and fMRI spatially. ICA has been implemented for parallel decomposition of EEG and fMRI and joint ICA of the multimodal data. It is important to note that this involves a strong assumption that the linear covariation for both modalities is the same. However, it has the advantage of providing a parsimonious way to link multiple data types (fusing ERP and haemodynamic data) as demonstrated by V D Calhoun, Adali, Pearlson, & Kiehl, 2006. 3.2.1 Application to EEG-fMRI at 9.4T This decade has had several firsts. So was for EEG-fMRI, Neuner et al. who investigated the feasibility of recording EEG inside a 9.4 T static magnetic eld, specically to determine whether meaningful EEG information could be recovered from the data after removal of the cardiac-related artefact using ICA. The progression to higher eld strengths will not affect the temporal resolution of the EEG, therefore, it is still as valuable as it was at lower eld strengths. Also, fMRI signals will be acquired at ultra-high elds resulting in increased localisation and sub-millimetre precision. The price to be paid, however, is with the simultaneous acquisition. Artefacts from fMRI gradient switching as well as physiological cardiac artefacts will contaminate the EEG signal (Mullinger, Brookes, & Stevenson, 2008). The artefact resulting from gradient switching can be corrected for rather easily. This s because it is generated by the MR scanner and will therefore be consistently reproducible across a session (Allen, Josephs, & Turner, 2000). The cardiac artefacts are naturally far more variable. Neuner et al. were able to correct for the cardiac-related artefact and identify auditory event-related responses at 9.4 T in 75% of subjects using ICA. This shows that ICA is opening up new horizons for research questions that were hitherto extremely difficult to address. 3.3 Application to fNIRS

Zhang et al. showed that ICA is an excellent method for the detection of resting-state brain functional connectivity from fNIRS measurements. They show that ICA performs better than the traditional approach (seed correlation) and achieves this with higher sensitivity and greater specificity. ICA was also effective in cleaning artefacts from the data thereby 7

producing reliable functional connectivity results. Therefore, in totality ICA seems to be a promising approach to investigate functional connectivity based on fNIRS (Zhang et al., 2010). 3.4 Application to source characterization

ICA has been widely accepted to remove artefactual data from EEG and other neuroimaging data. However, its use to isolate and characterize cortical sources only just beginning to increase. It can be said that the far-field signal that arises from a patch of local spatiotemporal field synchrony should nearly be independent from any such signal that arises anywhere else in the cortex and the net far-field projection of such a patch of cortex will be nearly equal to a single equivalent current dipole located in the vicinity or ideally beneath the generating cortical patch (Delorme, Palmer, Onton, Oostenveld, & Makeig, 2012). This concept does not seem counterintuitive and can be explained by the high anatomic bias in cortical connectivity toward connections in the vicinity (<100m) along with the radial connectivity between cortex and the thalamus. Hence, decomposition into components with maximally independent time courses (ICA) in practice, can return up to dozens of maximally independent components whose scalp maps could be generally compatible with their generation in a patch of cortex. Delorme et al., 2012 for the very first time demonstrate using that linear BSS algorithms, ICA decompositions in particular do in fact return components with more near-dipolar scalp maps. Furthermore, the degree of efficiency in reducing mutual information among the decomposed component time courses is shown to be positively correlated with the number of biologically plausible near-dipolar components returned by the algorithm. Also, this relationship seems to be on average, linear. This is a very curious result that invites closer inspection.

Concluding Remark
ICA can successfully and efficiently separate the what (source signals and artefactual signals) from the data and is well on its way to improve our ability to possibly answer the inverse problem of finding where the source signals originated.

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