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: + + + \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. + + Additionally you have the option to create artificial networks, for testing purposes. Currently choices are: */ /** \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: Furthermore some statistics are calculated on a per node basis and displayed as histograms: */