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| ''Authors: Yaqi Li, Helen Lin'' <<BR>> This tutorial will guide the user through the usage of all the features available in the connectvity visualization tool. This tool displays functional connectivity data in the form of a 'graph' suited for human understanding. For a theoretical background on functional connectivity, please refer to <<GoTo>>. <<TableOfContents(2,2)>> |
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| We will begin this tutorial by loading a connectivity graph. Please go through the following steps: <<BR>> |
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| 3. Next, ensure that the '''scout function is applied Before.''' You may also choose a desired atlas. For this tutorial, choose Mindboogle. | <<BR>> 3. Next, ensure that the '''scout function is applied Before.''' You may also choose a desired '''atlas'''. To do so, ensure that the "Use scouts" option at the top left is selected. The atlases can be found in the drop down menu shown on the top right. For this tutorial, choose "Mindboogle". |
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| Nodes are labeled along the circumference of the graph. Connections are represented by coloured lines. Connectivity scores are represent through a colormap, which you can see in the colorbar on the bottom right of the figure. 5. The steps in the following sections will guide you through the display options available in this tool. |
<<BR>> The steps in the following sections will guide you through the display options available in this tool. <<BR>> == Connectivity graph structure == In this visualization tool, the connectivity scores from the connectivity matrix are shown as links drawn between regions of interest. As shown in the previous figure, these regions of interests are displayed as nodes are labeled along the circumference of the graph. They are grouped in their respective lobes (such as "Frontal", "Cerebral", etc. shown in the figure above) and hemispheres (i.e., left and right hemisphere). Connections are represented by coloured lines. Connectivity scores are represent through a colormap, which you can see in the colorbar on the bottom right of the figure. <<BR>> The graph used throughout this tutorial is built with the Mindboogle brain atlas, which generates the labeled nodes shown in the previous figure above. Note that the lobe and node structure will vary according to the atlas selected by the user. <<BR>> == Camera View == The mouse wheel can be used to zoom-in and zoom-out on the figure. Dragging the mouse while maintaining a left click also allows you to move the figure on your screen. The following steps will guide you through these options. <<BR>> 1. Move your mouse wheel to zoom-in and zoom-out. Below is an example of the figure being zoomed out. {{attachment:camera_zoom_out_jet.PNG}} <<BR>> 2. Now, press '''SHIFT''' and left click anywhere on the figure. Move the mouse while maintaining the mouse click and the SHIFT key pressed to drag the figure around. This camera feature allows you to focus on one area of interest in the figure. <<BR>> |
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| jjjj | This tool provides users with the option to display only links belonging to a particular set of nodes of interest. <<BR>> 1. In the popup menu, click on "'''Select next region'''". You should see all nodes belonging to one particular lobe being selected, while all other nodes become unselected. When a region of interest is selected, only nodes belonging to it appear as filled markers, while other nodes will be displayed with a 'x' marker and have their labels greyed out. The region being selected depend on the atlas selected. An example is shown below. Here, the right hemisphere is selected. <<BR>> 2. Click on "Select next region" again. You should see another region being selected. Continue doing so a few more times - the program will keep iterating through the different hemispheres, lobes and then the measure nodes. {{attachment:next_region_first.PNG}} <<BR>> 3. Click on "'''Select previous region'''". The program will iterate through the regions in the opposite order. 4. Now, click on "'''Select all'''" in the popup menu. You should see all nodes being selectd, and all links being displayed. <<BR>> |
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| Users also have the possibility to select specific nodes, lobes or hemispheres of interest through mouse clicks so as to only display links related to them. When a region of interest is selected, only nodes belonging to it appear as filled markers, while other nodes will be displayed with a 'x' marker and have their labels greyed out. | Users also have the possibility to select specific nodes, lobes or hemispheres of interest through mouse clicks so as to only display links related to them. Again, when a region of interest is selected, only nodes belonging to it appear as filled markers, while other nodes will be displayed with a 'x' marker and have their labels greyed out. <<BR>> |
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| == Link Selection == | <<BR>> == Link selection == |
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| Options appearing in the popup menu can also be toggled or selected with various keyboard shortcuts indicated to their right. For example, pressing "'''H'''" on your keyboard allows you to hide region nodes and pressing "'''M'''" on your keyboard allows you to display region links. | Options appearing in the popup menu can also be toggled or selected with various keyboard shortcuts indicated to their right. The '''SHIFT''' key must be pressed on the keyboard. For example, pressing SHIFT + "'''H'''" on your keyboard allows you to hide region nodes and pressing SHFT + "'''M'''" allows you to display the region links. |
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== Summary of features == You have now reviewed all feature of this visualization tool. The following table summarizes all the user-interactive features available in this tool. * Features highlighted in blue are also accessible in the popup menu. <<BR>> ''Table 1. Summary of features. '' {{attachment:summary_features_table_word_new.PNG}} |
Tutorial xx: Connectivity Graphs
Authors: Yaqi Li, Helen Lin
This tutorial will guide the user through the usage of all the features available in the connectvity visualization tool. This tool displays functional connectivity data in the form of a 'graph' suited for human understanding. For a theoretical background on functional connectivity, please refer to