diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox
index 16a5f3da53..fa344b2985 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox
@@ -1,89 +1,108 @@
/**
\page org_mitk_diffusionimagingapp_perspectives_connectomics The Connectomics Perspective
\image html connectomics_perspective.png "Icon of the Perspective"
The connectomics perspective is a collection of views which provide functionality for the work with brain connectivity networks. Currently there exist the following views:
\subpage org_mitk_views_connectomicsdata provides network generation either from data or synthetically.
\subpage org_mitk_views_connectomicsnetworkoperations provides functionalies to operate and process on networks and other data.
\subpage org_mitk_views_connectomicsstatistics provides statistical measures for networks.
+\section org_mitk_diffusionimagingapp_perspectives_connectomicsNetworkRenderingCustomization Network Rendering Customization
+
+The rendering of the connectomics networks can be customized by changing the associated properties using the property list. A selection of possible options are:
+
+
+ - Connectomics.Rendering.Edges.Filtering - Only render edges above a certain threshold
+
- Connectomics.Rendering.Edges.Gradient.Parameter - Color the edges according to certain parameters
+
- Connectomics.Rendering.Edges.Radius.Parameter - Change the radius of the edges according to certain parameters
+
- Connectomics.Rendering.Nodes.Filtering - Only render nodes above a certain threshold
+
- Connectomics.Rendering.Nodes.Gradient.Parameter - Color the nodes according to certain parameters
+
- Connectomics.Rendering.Nodes.Radius.Parameter - Change the radius of the nodes according to certain parameters
+
- Connectomics.Rendering.Scheme - Switch between the MITK rendering scheme using above properties and the very fast, but less customizable rendering scheme for VTK graphs
+
+
\section org_mitk_diffusionimagingapp_perspectives_connectomicsTrouble Troubleshooting
No known problems.
All other problems.
Please report to the MITK mailing list.
See http://www.mitk.org/wiki/Mailinglist on how to do this.
*/
/**
\page org_mitk_views_connectomicsdata The Connectomics Network Data View
\image html QmitkConnectomicsDataViewIcon_48.png "Icon of the View"
This view can be used to create a network from a parcellation and a fiber image as well as to create synthetic networks.
\image html dataview.png "The user interface"
To create a network select first a parcellation of the brain (e.g. as provided by freesurfer ) by CTRL+Leftclick and secondly a fiber image ( as created using a tractography view). Then click on the "Create Network" button.
+
+ - "Use label of end position of fibers" will create a network containing a node for every label a fiber ends in
+
- "Extrapolate label" will avoid creating nodes using FreeSurfer white matter labels and instead extrapolate in which grey matter label the fiber would end
+
+
Additionally you have the option to create artificial networks, for testing purposes. Currently choices are:
- A regular lattice, where each node is placed in a cubic pattern and only connected to its neighbours
- A heterogenic sphere, where one node is placed in the center and connected to all nodes on the shell
- A random network, where nodes are randomly placed on a spherical shell and randomly connected
*/
/**
\page org_mitk_views_connectomicsnetworkoperations The Connectomics Network Operations View
\image html QmitkConnectomicsNetworkOperationsViewIcon_48.png "Icon of the View"
This view can be used modify networks and related data.
\image html operationsview.png "The user interface"
Select a parcellation and press "Convert to RGBA" to create a RGBA image. By doing this conversion it is much easier to discern the different parcels. Furthermore MITK supports 3D visualization of an RGBA image.
Select a network and press "Create Connectivity Matrix Image" to create a 2D image of the connectivity matrix. By default the weight of a connection is used as grey value. Using the "Rescale" option will rescale the weights so highest one is 255. Using the "Binary" option will result in a binary connectivity matrix.
*/
/**
\page org_mitk_views_connectomicsstatistics The Connectomics Statistics View
\image html QmitkConnectomicsStatisticsViewIcon_48.png "Icon of the View"
This view can be used to show statistical analysis of a network.
\image html statisticsview.png "The user interface"
To calculate network statistics select a network in the datamanager. At this time the following statistics are calculated for the entire network:
- The number of vertices in the network
- The number of edges in the network
- The number of edges which have the same vertex as beginning and end point
- The average degree of the nodes in the network
- The connection density the network (the number of edges divided by the number of possible edges)
- The unweighted efficiency of the network ( 1 divided by average path length, this is zero for disconnected graphs)
- The global clustering
Furthermore some statistics are calculated on a per node basis and displayed as histograms:
- The degree of each node
- The (unweighted) betweenness centrality of each node
- The spread of shortest paths between each pair of nodes (For disconnected graphs the shortest paths with infinite length are omitted for readability)
*/