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<h1>OpenWalnut Help <img src="icons/logoIcon.png"/></h1>
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<h2>Contents</h2>
<ol>
<li><a href="#Introduction">Introduction</a></li>
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<li><a href="#FirstSteps">First Steps</a></li>
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<li><a href="#MainWindow">Main Window</a></li>
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<li><a href="#Navigation">Navigation</a></li>
<li><a href="#Keyboard">Keyboard Shortcuts</a></li>
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<li><a href="#Toolbar">Toolbar</a></li>
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<li><a href="#ROIs">Regions of Interest</a></li>
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<li><a href="#Config">Customizing OpenWalnut</a></li>
</ol>

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<h2><a name="Introduction" />Introduction</h2>
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The intention of this help document is to give a short overview of how to use the current version 
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of OpenWalnut. Although it is not at all comprehensive, 
it provides a description of the most commonly used features and GUI elements. 
As described <a href="#Config">below</a>, the appearance of the GUI is customizable. This help document 
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assumes the standard configuration. Additionally, some described features may not be available 
in every instance of OpenWalnut because they belong to special modules.
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<h2><a name="Introduction" />First Steps</h2>
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<a href="http://www.openwalnut.org/projects/openwalnut/wiki/FirstSteps">This</a> tutorial shows you the basic useage of OpenWalnut. You should consider reading this if you are a first time user.
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<h2><a name="MainWindow" />Main Window</h2>
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This is the main window of OpenWalnut. It is divided in three parts. The navigation views, the main view and the data manipulation GUI.
<img src="images/2_overview.png"/>
<ul>
<li> 1,2, and 3 - The navigation windows. Use them for orientation and and current position.
<li> 4 - The main view. The main view allows interaction with the visualization and the camera in 3D.
<li> 5 - The module tree. This shows the current setup of your data flow. Use this to process data and to apply visualization.
<li> 6 - The control panel. This shows parameters and further information of the currently selected module. Use this to interact with your
modules.
</ul>
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<h2><a name="Navigation" />Navigation</h2>
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<h3>Navigation in Main View</h3>
<table>
<tr><td><b><i>Mouse Button&nbsp;&nbsp;</i></b></td><td><b><i>Action</i></b></td></tr>
<tr><td>Left</td><td>Rotate</td></tr>
<tr><td>Middle</td><td>Pan</td></tr>
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<tr><td>Right</td><td>Pick, move <a href="#ROIs">ROI</a> box, or move slice</td></tr>
<tr><td>Right + [Shift]</td><td>Resize <a href="#ROIs">ROI</a> box</td></tr>
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<tr><td>Wheel</td><td>Zoom</td></tr>
<tr><td><b><i>Key</i></b></td><td><b><i>Action</i></b></td></tr>
<tr><td>+</td><td>Zoom in</td></tr>
<tr><td>-</td><td>Zoom out</td></tr>
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<tr><td>[Space]</td><td>Reset view</td></tr>
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</table>
<h3>Navigation in EEG View</h3>
<table>
<tr><td><b><i>Mouse Button</i></b></td><td><b><i>Action</i></b></td></tr>
<tr><td>Left</td><td>Mark event position</td></tr>
<tr><td>Middle</td><td>Pan</td></tr>
<tr><td>Right</td><td>Zoom in time</td></tr>
<tr><td>Wheel</td><td>Scale voltage</td></tr>
<tr><td>Wheel + Right</td><td>Change spacing between graphs</td></tr>
<tr><td>Wheel + Left</td><td>Change sensitivity of the coloring of the head surface</td></tr>
</table>
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<h2><a name="Keyboard" />Keyboard Shortcuts</h2>
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<h3>Program-wide Keyboard Shortcuts</h3>
<table>
<tr><td><b><i>Key</i></b></td><td><b><i>Action</i></b></td></tr>
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<tr><td>[Ctrl] + q</td><td>Quit</td></tr>
<tr><td>[Esc]</td><td>Resets main view</td></tr>
<tr><td>[F1]</td><td>Opens help window</td></tr>
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</table>
<h3>ROI tree</h3>
<table>
<tr><td><b><i>Key</i></b></td><td><b><i>Action</i></b></td></tr>
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<tr><td>[Delete]</td><td>Removes <a href="#ROIs">ROI</a></td></tr>
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</table>
<h3>Module tree</h3>
<table>
<tr><td><b><i>Key</i></b></td><td><b><i>Action</i></b></td></tr>
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<tr><td>[Delete]</td><td>Removes module</td></tr>
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</table>

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<h2><a name="Toolbar" />Toolbar</h2>
<table>
<tr><td><b>Icon</b></td><td><b>Name</b></td><td><b>Description</b></td></tr>

<tr><td><img src="icons/fileopen.png" width="20"></td><td>Load
    Data</td><td>Loads data given in various formats like fibers (.fib), NIfTI
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    images (.nii, .nii.gz) or EEG data (.cnt). Not all supported file formats
    are available through this button and the dialog behind it. For some file
    formats there are special modules for reading and/or writing them.</td></tr>
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<tr><td><img src="icons/projOpen.png" width="20"></td><td>Load a project from
    file</td><td>Opens a project file (.owp), and instantiates modules, sets their
    connections and orients the scene accordingly.</td></tr>
<tr><td><img src="icons/disc.png" width="20"></td><td>Save current project to
    file</td><td>Saves the current state (modules, connections, orientation of
    the scene) of OpenWalnut to a project file (.owp).</td></tr>
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<tr><td><img src="icons/camera.png" width="20"></td><td>Reset main view</td><td>Rotates
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    and scales the scene in the central 3D view to show the same orientation as
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    after program startup but zoomed to show all contents of the
    scene.</td></tr>
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<tr><td><img src="icons/box.png" width="20"></td><td>Create new
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    ROI box</td><td>Adds a new ROI box to the 3D scene and the ROI browser. See also: <a href="#ROIs">ROIs</a>.</td></tr>
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<tr><td><img src="icons/QuestionMarks.xpm" width="20"></td><td>Missing
    module?</td><td>This opens the dialog that allows to customize the list of
    modules that are allowed to appear in the <i>Compatible Modules</i> toolbar.</td></tr>
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</table>

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<h2><a name="ROIs" />Regions of Interest</h2>
A ROI (<b>r</b>egion <b>o</b>f <b>i</b>nterest) is usually used to specify a
certain area (2D) or volume (3D) that can then be accessed by
modules. Different modules will use ROIs for different purposes. The most
important purpose of ROI boxes in OpenWalnut is the selection of fibers in
conjuction with fiber display modules. It will be described in a separate
section below.

The ROIs can be moved around by dragging them with the right mouse
button. Their size can be changed by dragging one of their faces with the right
mouse button while the [Shift] key is pressed.

<h3>ROIs for selecting fibers</h3>
For the special task of selecting fiber bundles from larger sets of fibers ROIs can be
combined in the ROI tree widget. All ROIs in the same branch of the tree are
combined using a Boolean "and" operation. The result will be a bundle
consisting only of fibers that pass through all boxes in the branch. The branches themselves are combined
using a Boolean "or" operation. This means that the bundles selected by the
different branches will be visible/selected at the same time.

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<h2><a name="Config" />Customizing OpenWalnut</h2>
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OpenWalnut allows you to configure several features. Most of these options are
only useful to advanced users. Have a look into the <i>View</i>, <i>Camera</i> and <i>Settings</i>
menus for what you can adapt. If you would like to configure which modules are
allowed to be shown in the toolbar click on the <tt>Missing Module?</tt> button
with the three question marks. The appearing dialog will provide enough information
and the possibility to customize which modules may appear. This can be useful
to maintain a not too crowded toolbar.
<br />
<br />
<font color="#aaa">
<small><b>For more information on OpenWalnut
  visit <a href="http://www.openwalnut.org">www.openwalnut.org</a>.</b></small>
</font>
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