Illustrative visualization for structural connectivity and cortex parcellations

Requirements

• an installed OpenWalnut, latest revision from branch "IllustrativeConnectivityVisualization", since the module uses some special features not yet available in the official OpenWalnut.
• an OpenGL and OpenCL capable graphics card (the newer the better, >2GB VRAM recommended) with updated drivers

Required data

• fiber data (binary vtk polydata file ending in .fib)
• a scalar dataset containing a region ID per voxel (NIfTI)
• a file containing color and name information for all IDs found in the region dataset
• a set of .png images to use as content of the labels (for freesurfer parcellations, these can be downloaded below)

The color and name information needs to be formatted in the following way (separated by spaces, one region per line):

ID type name r g b a

Example:

8 2 Thalamus-right 0 0.7 0 1

The type can be either 1 (white matter), 2 (grey matter) or 3 (rest).

Getting the source

The source code of the visualization module can be downloaded here:

• Connectivity visualization - zip version
• Connectivity visualization - tgz version

Additional resources:

• Label images for freesurfer parcellations - zip version
• Label images for freesurfer parcellations - tgz version

Installation

• make sure OpenWalnut is installed correctly (note that we are currently investigating issues with installing OpenWalnut under windows)
• unpack the content of the archives to a seperate directory
• navigate to the build folder inside the toolbox
• start cmake-gui and choose the "src" directory as source dir (found in the toolbox folder)
• press configure
• if necessary, input the correct paths to your OpenWalnut installation and press configure again
• press generate
• exit cmake-gui and start building via the build system of your choise (usually make)
• start OpenWalnut and add the path to the generated .so or .dll (windows) file inside the modules subfolder in the build/share folder inside the toolbox folder
• restart OpenWalnut

Usage

Generating the cluster data

• load both fiber and region data
• do not forget to set the correct transformation for the region data (click the data module, set "qform" as the transformation)
• add the "Calculate connectivity graph" module and choose the color and name information file
• connect the outputs of the region and fiber data to the respective inputs in the connectivity graph module

The resulting data can be save using the "Save cluster data" module.

Starting the visualization

• add the "Visualize fiber clusters" module
• connect the connectivity graph to the module

Optionally, structural data can be loaded and added via the second input.