Welcome to the Brain Atlas tutorial. Here you will find the basic steps for you to navigate through the Brain Atlas package.
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- Below, you can see an empty Brain Atlas interface.
- You can access via terminal by using the command:
- GUIElement(‘PE’, BrainAtlas()).draw()
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- You can open a Brain Atlas object previously saved by clicking in the File menu and using the Open option.
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- Or you can import your Brain Atlas from a file, by clicking in the Import menu and using the file extension option your file has. The file extensions can be .txt, .xls, or .json.
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- You can see the loaded information from your file in the GUI. You can edit the ID, Name, and Notes fields. You can see the brain region’s information in the table Brain Regions.
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- Using the right-click button on your mouse will show a table menu, where you can select all brain regions, clear the selection, invert the selection or apply an action to the selection. You can also export the selected brain region rows information to .xlsx format. If you have not selected or have selected all, all the fields will be exported.
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- Click on the plot brain atlas button to open the brain atlas surface with the brain regions in a new figure. In the toolbar you can choose from 7 different views, here we chose axial dorsal. You can also show or hide the brain surface, the axis, and the axis grid.
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- In the same toolbar, you can also choose to view your brain regions as spheres, symbols, ids, or labels.
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- To further edit your brain surface use the settings panel button which will open all the available properties of the figure, the brain atlas surface, and the brain regions. Here we fixed the figure background color to gray, we kept lighting to gourand, changed the material to dull, and removed the lighting. Finally, we changed the shading to interp and chose the colormap as cooper. The brain regions are shown as spheres.
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- Change the brain region representation by using the table corresponding to the type of brain region representation. Here, we hide the spheres and show the symbols. Using the table we select half the brain regions and change the size, color, and shape.
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- Finally, you can save the figure or print it ready for publication. To print click the Print menu and select the desired resolution and format.
