\chapter{Materials and Methods}
\label{mat}
\section{Scientific background}
\label{mat:background}
    \subsection{BCIs}
        The idea of BCIs began to spread in the 1970s when Vidal published his paper (\cite{Vidal73}).\\
        First approaches used invasive BCIs earlier in Animals (rodents and monkeys) later also in humans. Invasive BCIs in humans were mostly implanted when the human was under brain surgery for another reason like therapy of epilepsy. Problems of invasive BCIs are the need to cut through skull and dura mater. This can lead to infections and severe brain damage.\\
        An improvement were less invasive BCIs with e.g. ECoG which is placed inside the skull but outside the dura which decreased the risk for infections massively.\\
        Measuring outside the skull entails even less risk, the dura and skull however lower the quality of the signal massively. With some improvements EEG has a spatial resolution of 2-3 cm (cf. \cite{Babiloni01}). This is quite bad compared to the single neuron one can observe with invasive methods. However we are more interested in the activity of areas then single cells for our task, so EEG meets our requirements here.\\
        In addition EEG is much cheaper and easier to use than other techniques. There is no need for surgery (like for invasive methods) and the hardware can be bought for less than 100\euro{} while FMRI hardware costs far above 100,000\euro{}. This is one of the reasons EEG is far more available than other techniques. There are some inventions of younger date but not as much work has been done with them why they aren't as well known and as far distributed as EEG.\\
        Another pro of EEG is that the device is head mounted. That means the user may move while measuring without high impact on the tracking of activity. This is highly necessary for any BCI used in daily life.
    \subsection{EEG}
        When using Electroencephalography (EEG) one measures the electrical fields on the scalp that are generated by activity of neurons in the brain. These measurements allow some interpretation about what is happening inside the skull. In our application we use the recorded currents directly to train a SVM or as predictor for regression.

        The foundation stone for EEG was laid in 1875 when Richard Caton found electrical activity around the brain of monkeys. After testing the methods on animals in 1924 the first human EEG was recorded by Hans Berger in Jena. He also coined the term Electroencephalography and is seen as the inventor of EEG.

        The frequencies typically used for movement prediction in EEG are about 8-24 Hz (\cite{Blokland15},\cite{Ahmadian13},\cite{Wang09}).
        EEG is often used for non-invasive BCIs because it's cheap and easier to use than e.g. fMRI. The electrodes have to be spread over the scalp. To allow for comparability there are standardized methods for this. These methods also bring a naming convention with them.
        \subsubsection{10-20 system}
            In this standard adjacent electrodes are placed either 10\% or 20\% of the total front-back or left-right distance apart. This standardization also makes it possible to name each electrode or rather here place. This is done with capital letters for lobes (Frontal, \qq{Central}, Parietal, Occipital and Temporal) and numbers for the specific place on the lobe. Even numbers are on the right side of the head, odd on the left; larger numbers are closer to the ears, lower numbers closer to the other hemisphere. The exact number now refers to the exact position: $$\left\lceil\frac{x}{2}\right\rceil\cdot \frac{d}{10}$$ where $x$ is the number and $d$ the diameter of the scalp. Electrodes in the centre are named with a lower case $z$ e.g. $Cz$.\\
            Electrodes between two lobes (10\% instead of 20\% distance) are named with the both adjacent lobes (anterior first) e.g. $FCz$ (between frontal and central lobe).
            Also see figure~\ref{fig:10-20}.
        \begin{figure}[!p]
            \centering
            \includegraphics[width=\textwidth]{eeg_electrodes_10-20.png}
            \caption{Full 10-20 system}
            \label{fig:10-20}
        \end{figure}
        \subsubsection{\texttt{pburg}}
        \label{mat:pburg}
            For power spectral density estimation (PSD) of the EEG signal we used MATLAB's pburg method. This uses Burg's method, a parametrized method of PSD.\\
            %... see bookmarks
    \subsection{Low Frequencies}
        Another approach is looking at the low frequency features (below 2Hz) in the signal. This was done by Liu et al. (\cite{Liu11}) and Antelis et al. (\cite{Antelis13}) for example.\\
        Antelis et al. found correlations between hand movement and low frequency signal of $(0.29,0.15,0.37)$ in the dimensions respectively.
        %TODO: more details (idea, possible explanantion)
    \subsection{EMG}
        Electromyography (EMG) is used to track muscle activity. This is done by measuring the electrical fields on the skin generated by muscle contraction. %TODO
    \subsection{Synergies}
        Movement of the arm (and other parts of the body) are under-determined meaning with given trajectory there are different muscle contractions possible. One idea how this problem could be solved by our nervous system are synergies. Proposed by Bernstein in 1967 (\cite{Bernstein67}) they describe the goal of the movement (e.g. the trajectory) instead of controlling single muscles. This would mean however that predicting the activity of single muscles from EEG is harder than predicting a synergy which in turn determines the contraction of muscles.\\
        Evidence for the use of synergies in the nervous system was found e.g. by Bizzi et al. (\cite{Bizzi08}) and Byadarhaly et al. (\cite{Byadarhaly12}). They also showed that synergies meet the necessary requirement to be able to build predictable trajectories.\\
        Synergies are usually gotten from EMG signal through a principal component analysis (PCA, cf. \ref{mat:pca}), non-negative matrix factorisation (NMF, cf. \ref{mat:nmf}) or autoencoders (a form of neuronal network, cf. \ref{mat:autoenc}).
    \subsection{Autoencoders}
    \label{mat:autoenc}
        Autoencoders are a specific type of artificial neural networks (ANN). They work like typical ANNs by adjusting weights between the layers however they don't predict an unknown output but they predict their own input. What is interesting now is manipulating the size of the hidden layer where the size of the hidden layer has to be smaller than the input size. Now in the hidden layer the information of the input can be found in a condensed form (e.g. synergies instead of single muscle activity).\\
        Autoencoders have been successfully used by Spüler et al. to extract synergies from EMG (\cite{Spueler16}). Especially with a lower number of synergies autoencoders perform better than PCA or NMF because linear models fail to discover the agonist-antagonist relations that are typical for muscle movements. These however can be detected by autoencoders which allows for good estimations with half the synergies.
\subsection{PCA}
\label{mat:pca}
\subsection{NMF}
\label{mat:nmf}