If the applet does't run ...
The online version of the Brain Navigator is a Java
applet, a small program capable to run inside your Web browser
window. To make this possible you must have installed the Java
runtime (1.4x or newer) on your computer. If you don't have already
done so please install Java on your computer (available free of
charge for several platforms from Sun (http://java.sun.com/j2se/downloads.html).
We tested the Navigator applet with Linux and several Windows
versions using Firefox, Opera and Internet Explorer. It should also
run on MacOs X (with Java 1.4) but we didn't test this. For telling
us your experiences or problems with the Navigator applet please use
our contact
form.
Please also check your browser preferences and make sure to allow
Java inside a Web page!
Normal appearance of the Navigator applet
 If
everything is correctly installed the Navigator applet should load
(indicated by a moving bar) and - after some time (dependent on your
internet connection speed) -
finally start up with two windows looking like the following:
One is a popup window and can be moved around with the mouse. It
shows a colorful schematic frontal brain slice and the names of
structures under the mouse pointer. The popup window may be
hidden behind your main browser window. You can bring it on top or
hide it with a button. Please place it somewhere on
your screen, where it doesn't overlap with other windows. The big
window is used for navigation through the brain. It shows a coronal,
a horizontal and a sagittal cut through the brain. The point
of interest is indicated by a crosshair. Click anywhere inside one
of the views to change the position. Note that the image displayed
in the popup window changes synchronously (it always shows the right
hemisphere of the actual coronal slice). Sequentially moving through
a series of slices is also possible. Press the button indicating
your desired orientation (C=coronal, H=horizontal, S=sagittal) and
move the slider with the mouse or click on the arrows.
Zero brings you back to the anterior commissure (the origin
of the coordinate system). For more about coordinates please read
the following
chapter.
Some features like ShowHistology and SubCx (=Subcortex)
are only available in the full version of the Navigator (coming with
the printed Atlas of
the Human Brain, 2nd ed. - if you own this book please don't use
the program from CD, download your free update from www.thehumanbrain.net/navigator/update
instead.)
The Navigator applet only demonstrates these features and displays some
information.
The switch (photo | plate) allows to view the original
stained slice (photo) instead of of the colored schema (plate) in
the popup window and vice versa. Note that unlike the full version the applet only includes
few photos.
Why coordinates and how to enter them
Every point in the atlas space is a 3d coordinate. You can use
this coordinate to directly jump to a specific place in the brain or
to lookup or reference a structure at a given position.
The Navigator uses two coordinate systems: The Atlas of the Human
Brain system and the Talairach system. Both have the same
origin but differ in detail. It is possible to switch between these
two systems and to enter coordinates directly. For this the
following multipurpose panel is used:
The x, y and z fields tell you the position of the crosshair in mm
using the coordinate system indicated below (here: Atlas of the
Human Brain). Please click on the Change button to switch to
Talairach system and back. If you are moving your mouse above the
popup window don't be surprised because the values of the
fields change to show the actual position of the mouse pointer. If
the mouse leaves the popup window the original values are
restored.
To directly enter coordinates click on the x, y or z-field and type
in a new position. (Use the English numeric notation, don't use a
comma). Press the Enter key or click on a different field to
complete. The crosshair now moves to the new position and different
brainslices are shown. Note: Because The resolution of the Navigator is
limited the coordinates you entered may be changed slightly to a
nearby value.
Sometimes the entry of more than one point is necessary, e.g. if
data from literature shall be compared with own findings. For this
purpose a special entry
form (www.thehumanbrain.net/navigator/coordinates.htm)
can be used together with the Navigator applet. (Please make sure to
allow JavaScript in your browser preferences before using this
form!)
First choose your coordinate system (Talairach or Atlas of
the Human Brain) Then type in your x, y and z-coordinates into
the respective fields. You may choose a label for every point. Click
on 'Add Coordinate' to add your data to the list. Continue with
additional points or click on 'Import into Navigator' . The
Navigator then takes your data and shows every point as a small
circle. The crosshair will be placed on your first datapoint. If you
place the mouse cursor on one of the circles in the popup window
your label will be displayed at the bottom.
 Try
the button 'Import Demo Coordinates. A big number of circles appear
derived from several functional MRI studies. The red circles belong
to the right hemisphere, the green circles to the left. This color
code has been necessary, because in the popup window only the right
hemisphere is shown. In this window the data from the left
hemisphere is mirrored and shown in green. If you click on one of
these circles the crosshair is adjusted to the center of the circle
in all 3 views. (If you click on a circle from the demo dataset
additional information about the referenced study is displayed in a
separate window).
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