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Java-based Exploratory Data Analysis for EEG
Welcome
This Java-based application can be used for performing a range of signal
processing operations on EEG data files, up to and including visualization
and scoring of spectra and ERPs.
It can be used for analysis of EEG recordings obtained from several
sources, including files in EDF format. This program has a special
relevance to members of
BRAINnet —
the group of researchers with a common focus on the wide-ranging body
of brain function data provided through BRAINnet. Jeda is the means to
perform fully-customized analyses on EEG files in the BRAINnet database.
The problem with EEG analysis is not that it is difficult, but
that it is awkward. It is awkward due to the multitude of formats
and the diversity of analysis strategies for time-series data, both of
which discourage the development of standard analysis tools. The present
application addresses these problems by providing a framework
for EEG analysis, which hard-codes routine jobs while relying on scripts
and plug-ins to accomodate innovation.
The scripts and plug-ins help to modularize the problem of EEG analysis;
and help in testing, comparing and sharing of methods.
The application is not for everyone. Its size and wide-ranging goals
result in a complexity that may be offputting. However its modularity
and batching capability should appeal to anyone involved in specialized
and/or large-scale EEG processing.
There are presently two versions of Jeda available:
- The 'detailed' version, which requires compilation and comes with
only a few datasets: see Introduction to Jeda
- The 'demonstration' version, which is pre-compiled and comes with a
large number of datasets, but is minus certain complications:
see below
The most up-to-date version of the documentation can be found at
www.brain-dynamics.net/jeda/index.html
The documentation for Jeda is in four parts:
An easy way to see Jeda in action is to:
- Confirm that you have Java installed, that the version is
1.5.0 or later, and that certain environment variables are set.
See Java installation instructions
for details of how to do this.
- If you have the demonstration version on a CDROM, then Window's
'autorun' feature means that simply inserting the disk
should cause the program to run.
- Alternatively, if you have copied the demonstration version of Jeda
to your hard disk (or 'autorun' fails, or you have some other version
of Jeda on hard disk), then you will need to run the program manually:
- Open a terminal window
- Change to the directory containing the distribution
- Run the demonstration by typing ./demo (if Linux) or
demo (if Windows). (This runs a batch file, demo
or demo.bat, which in turn runs Java.)
- A small window 'Demo of Jeda' will appear, which provides a simple
GUI front-end to Jeda. Choices can be made, and pressing 'Proceed'
will cause various graphics various graphics to be generated.
A few things may go wrong …
- Maybe you downloaded Jeda as an ISO file. In this case you should
make the contents accessible either (a) by copying the ISO to a
CDROM, or (b) by 'mounting' the ISO. Under Linux mounting is achieved
by a command similar to
sudo mount -o loop jeda.iso /media/cdrom0
however under Windows some extra utility is required. A simple
utility is available from Microsoft for Windows XP: Google for
'winxpvirtualcdcontrolpanel_21.zip'. After unzipping
you will see three files: a .exe program, and .sys driver, and
a readme file containing instructions.
- Sometimes autorunning batch scripts on CDs is blocked by the
operating system. If so, try running the program manually
(as described above).
- Java is highly portable. However there may be obscure special
case related to multiple screens, small RAM size, unusual mouse
devices, etc, that cause problems.
- Maybe there will be a terminal screen visible only briefly, and
then it vanishes. This is a sign that autorun is being attempted,
but Java couldn't be found. If this happens, then look at the more
detailed
installation instructions
for Java.
Note: Launching the demonstration program manually via a
GUI-based file browser is also possible. However this method
precludes the use of extra command line switches, and prevents easy
viewing of error messages. If manual running of the program is
necessary (and it is necessary for the detailed version), then
some familiarity with command line operations is advantageous.
The GUI allows choice of
- Either of two subjects: 81237443-1 or 81567509-1
- One of three referencing options: A1A2, Av or Cz
- Paradigm: EO,EC,AH,ODDB,GNG,EYET,LET,WM,MAZE,PPI, or FACES
- View: Summary, Detailed, Spectra or ERPs
Each of the 2×3×11×4 combinations of choices results
in a window; most of which may be further examined by zooming, scrolling,
popups etc. (Press 'H' to see the options.) Multiple windows can be
generated and displayed simultaneously.
A full description of the eleven paradigms mentioned above is available
to BRAINnet members. Visit BRAINnet
to learn about how to become a member.
You must have the 22 raw data files (417MB) installed for
this demonstration to work. Look for a subfolder 'data' containing files
named '81237443-1.*.NS5' and '81567509-1.*.NS5'. The files are part of
the demonstration version. If you have some other version of Jeda, the
22 data file can be obtained as a separate download.