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Introduction

Clinical Neurophysiology is a medical field whose object is the study of the electrical activity generated (directly or indirectly) by the nervous system. In practice, clinical neurophysiologists are in charge of electroencephalography (EEG), electromyography (EMG), evoked potentials, sleep recordings and other analogous diagnostic tests. These pages are dedicated to these persons.

Clinical Neurophysiology has deeply changed with the introduction of computers. Polygraphs, electromyographs and other analogous instruments are now mounted on computers. At the core of these systems, files containing sampled data are stored, copied or processed.

Paradoxically, although files containing signals can be easily manipulated, the possibility to do that is strongly limited in practice. Modifications such as changing the algorithm applied to measure the amplitude of a response (base to peak or peak to peak, for instance) can be troublesome or even impossible. This situation is even worse when the user tries to develop some kind of analysis not previously implemented by the equipment.

Often the system does not contain information about the internal structure of data and, almost invariably, the user will have no access to the tools of development. If we compare the ability of a clinical neurophysiologist to treat a text, a sound or an image with his or her ability to manipulate neurophysiological signals, it is evident that there exists a wide gap.

Using software independent of the acquisition equipment would probably narrow this gap. These pages deal with some issues of signal treatment applied to Clinical Neurophysiology and intend to establish some bridges between :

  1. The ability to understand and design methods to analyze neurophysiological signals.
  2. The ability to use widely available software, not specifically designed to the analysis of neurophysiological signals, and
  3. The comprehension of some theoretical tools of signal treatment.

Why a clinical neurophysiologist could wish to treat signals?

EEG, EOG, EMG or polygraphic recording can be sampled and manipulated by computers without loss of information. The manipulation of these signals provides at least the following advantages:

Since neurophysiological signals have a lot in common with other signals, the knowledge of methods of treatment of these signals can contribute to the extraction of relevant information to our field.

What are the advantages of using free software and how to get it

The election of the software that we are going to use can be a risky operation. I suggest that you consider the possibility of ``free software''. Although there are some differences in the ``taxonomy'' of ``free software'', this term refers to software that can be legally copied and that is distributed with its sources. The freedom of using it spans to allow the modification of the code to fulfill your own requirements. Usually, ``free software'' is distributed free of charge.

Some programs widely recognized as excellent (Linux, emacs, latex, gimp...) belong to this category. From the point of view of the user, the utilization of this kind of software produces some subtle advantages that push forward his or her work, among them:

Free software is usually obtained by downloading from Internet sites or by installing from a Linux distribution. The election of the software that we will use is an important decision.

Probably, some characteristics of the program in question indicate that, most likely, it will be useful. Preferably a program should be:

In my opinion, Scilab is the right choice for the treatment of neurophysiological data: it is free, it contains source code (in Fortran, C and in its own language), it is powerful and very well documented, and it is reasonably easy to use.

In the next sections I will describe some characteristics of Scilab, trying to stress the possibilities of its use in a neurophysiological environment. These pages are directed to clinical neurophysiologists not necessarily formed in mathematics or programming.

Perhaps the best way of reading these pages is interactively with Scilab. You can check the examples in your own system and explore the wide possibilities of this package.



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j 2003-01-23