The Connectivity Visualization Tool

This application is also described in Shen et al, Nature Protocols 2017 – see in particular Figure 6. It was initially created for the needs of work published in Finn et al, Nature Neuroscience 2015 and Rosenberg et al, Nature Neusocience 2016. The default parcellation used is from Shen at al, NeuroImage 2013 and is available for download from our NITRC page.


Using the Application

To open the connectivitity visualization tool navigate to https://bioimagesuiteweb.github.io/webapp/connviewer.html.

The Connectivity Control.

Once the application is opened, you will be presented with a view as shown in the figure above. The Shen 268 region parcellation (Shen et al 2013) is loaded and a panel showing a circle plot (top left), a 3D view (top right) and the linked slice viewer bottom is shown.

This application can visualize two connectome matrices at once. These can be loaded as the Positive matrix and the Negative Matrix under the file menu. These should be binary files containing 1 or 0 and stored in .csv file (.txt also works but be careful). The program expects that the matrices are square and have the same dimensions as the underlying parcellation (e.g. 268x268 in the case of the Shen parcellation).

You may also select the AAL atlas instead from the Parcellations menu.

The Three Panels

The 3D Panels

The default display shows three linked panels as follows.

Clicking any point on the circle or the slice views will syncronize the 2 views and also place the cross-hairs in the appropriate location the 3D view.

Exploring the Application using the Sample Data

Under the Help menu select Load Sample Data as shown in the figure below

Load Sample Data

The connectome matrices are shown under A (these are simply binary matrices with red dots showing the connections). The currently selected node (B) is shown by a line from the center of the circles to its location on the circle, and its location is also shown in the 2D slices and 3D view.

To visualize a connectivity pattern, one uses the controls in the Connectivity Control which appears on the far right of the viewer and shown magnigied in the figure above. The options here are:

The Filtering Controls.

Given the number of edges in a connectome, it is impractal to visualize them all at the same time. The following controls enable the user to filter edges to highlight aspects of their data. An edge connects two nodes. It will be shown if at least one of the nodes satisfies the filtering criteria below.

Note: The Node, Lobe and Network entries are automatically updated each time the user clicks either in the circle view or the 2D view to select a node. The values of these are set by the properties of the current node.

The Drawing Options

Once the filters are set, the user may create the lines using the Create Lines button. The lines are additive, so if the user changes the filters and clicks Create Lines, the new lines will be drawn in addition to the old lines. To clear the lines use the Clear Lines button.

The Display Controls

The Display Controls

At the bottom of the connectivity control, there are some extra options under the Display tab. These are initially hidden but can be opened by clicking on the Display Tab as shown in the figure above.

These controls, control, how the lines are drawn (as opposed to the filtering controls which control which lines are drawn). The options are as follows:

There are also two buttons below these namely:

3D Modes

Using your Own Data

Parcellation

If your data was computed using the Shen et al parcellation or the AAL atlas, you may simply select this parcellation from the Parcellations menu.

Importing a parcellation as an image: You may import a parcellation either as an image or as a text file. In the case of an image, BioImage Suite Web expects an objectmap style image (in MNI space) where the value of each voxel is equal to the region it belongs to. To do this click on the option Import Parcellation as an Image under the Advanced Menu

Importing a parcellation as a text file: In this scenario, the user simply supplies the MNI coordinates of each node. This may be either a CSV or a text file with each node being specified on each line.

Parcellation Import

In both cases, once the import is completed, the user will be prompted to enter a description of the atlas and then to save it in a JSON format file with a .parc extension. In the future this file may be loaded using the Load Node Definition File under the File Menu

Connectome Matrices

This application can visualize two connectome matrices at once. These can be loaded as the Positive matrix and the Negative Matrix under the file menu. These should be binary files containing 1 or 0 and stored in .csv file (.txt also works but be careful). The program expects that the matrices are square and have the same dimensions as the underlying parcellation (e.g. 268x268 in the case of the Shen parcellation).

To load the first connectome matrix, simply use the Load Positive Matrix option under the File menu. If you would like to load a second matrix use the Load Negative Matrix option under the same menu. To clear the matrices use the option Clear Matrices also under the File Menu.

Visualizing the Connectome Matrices

You may also visualize the matrices, as matrices, using the option Show Matrices under the View menu as shown above.

Connectivity Information

Finally one can get information about the matrices using the option Show High Degree Nodes under the View menu as shown on the figure above. This will create a table a left sidebar (see figure above) showing the information about the top nodes. Clicking on any of the node entries in green will place the cross hairs of the viewer and circle on the particular node’s location.


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This page is part of BioImage Suite Web. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs, Dept. of Radiology and Biomedical Imaging, Yale School of Medicine.)