[ADD #530] some more help

doc/user/help/OpenWalnutHelp.html

@@ -8,17 +8,18 @@
 <li><a href="#Navigation">Navigation</a></li>
 <li><a href="#Keyboard">Keyboard Shortcuts</a></li>
 <li><a href="#Toolbar">Toolbar</a></li>
+<li><a href="#ROIs">Regions of Interest</a></li>
 <li><a href="#Config">Customizing OpenWalnut</a></li>
 </ol>
 
 
 <h2><a name="Introduction" />Introduction</h2>
-The intention of this help document is to give short overview of how to use the current version 
+The intention of this help document is to give a short overview of how to use the current version 
 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 
-asumes the standard configuration. Additionally, some described features may not be available 
-in every instance of OpenWalnut because the belong to special modules.
+assumes the standard configuration. Additionally, some described features may not be available 
+in every instance of OpenWalnut because they belong to special modules.
 
 <h2><a name="MainWindow" />Main Window</h2>
 By now this section only shows a snapshot of the main window of OpenWalnut. In
@@ -32,8 +33,8 @@ all components of the main window.
 <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>
-<tr><td>Right</td><td>Pick, move ROI box, or move slice</td></tr>
-<tr><td>Right + [Shift]</td><td>Resize ROI box</td></tr>
+<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>
 <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>
@@ -63,7 +64,7 @@ all components of the main window.
 <h3>ROI tree</h3>
 <table>
 <tr><td><b><i>Key</i></b></td><td><b><i>Action</i></b></td></tr>
-<tr><td>[Delete]</td><td>Removes ROI</td></tr>
+<tr><td>[Delete]</td><td>Removes <a href="#ROIs">ROI</a></td></tr>
 </table>
 <h3>Module tree</h3>
 <table>
@@ -77,24 +78,48 @@ all components of the main window.
 
 <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
-    images (.nii, .nii.gz) or EEG data (.cnt).</td></tr>
+    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>
 <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>
-<tr><td><img src="icons/camera.png" width="20"></td><td>Reset Main View</td><td>Rotates
-    and scales the scene in the cetral 3D view to show the same orientation as
+<tr><td><img src="icons/camera.png" width="20"></td><td>Reset vain view</td><td>Rotates
+    and scales the scene in the central 3D view to show the same orientation as
     after program startup but zoomed to show all contents of the
     scene.</td></tr>
+<tr><td><img src="icons/box.png" width="20"></td><td>Create new
+    ROI  box to the 3D scene and the ROI browser. See also: <a href="#ROIs">ROIs</a>.</td></tr>
 </table>
 
+<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.
+
 <h2><a name="Config" />Customizing OpenWalnut</h2>
 OpenWalnut allows you to configure several features. Most of these options are only useful to advanced users. 
-You can have a user-scope configuration in your HOME directory as ".walnut.cfg". 
+You can have a user-scope configuration in your home directory as ".walnut.cfg". 
 If this file exists, OpenWalnut loads this file. You can also specify a "walnut.cfg" in your OpenWalnut directory under 
-"share/OpenWalnut/". A default file will be there after installation. The dafault file is very well documented.
+"share/OpenWalnut/". A default file will be there after installation. The default file is very well documented.
 <br />
 <br />
 <small>For more information on OpenWalnut visit <a href="http://www.openwalnut.org">www.openwalnut.org</a>.</small>