# Brain Atlas

GUIBrainAtlas is a graphical user interface that allows the user to create a custom brain atlas or import one from data files in xml, txt, or xls format. GUIBrainAtlas provides numerous options to visualize the brain atlas and to manipulate brain regions. The brain atlas can be saved in a file *.atlas for future use within BRAPH; it can also be exported in txt or xml format for use within other applications.

Figure 1: Screenshot of GUIBrainAtlas. On the top there are the menu and the toolbar; below there are a table view (on the left) and a brain view (on the right) of the brain regions.

The layout of GUIBrainAtlas is shown in figure 1. It is composed of four main work areas:

• Menu permits one to access the basic functionalities of GUIBrainAtlas, including loading, saving, editing, and visualizing a brain atlas, as well as creating a cohort for further analysis.
• Toolbar gives direct access to some of the most commonly employed functionalities, in particualr loading, saving, editing, and visualizing a brain atlas.
• Table view shows the brain regions and their properties in a table. Permits one to select, add, remove, move, and edit brain regions and their properties.
• Brain view visualizes the brain regions on a brain surface. Permits one to adjust the visualization parameters. The brain image can be exported as a MatLab figure.

Example data and a tutorial video can be found on http://braph.org/videos/brain-atlas/

Getting Started

As a first example of the use of GUIBrainAtlas, we will proceed to import the Desikan brain atlas[1] from the Excel file desikan_atlas.xlsx. We will then proceed to modify the atlas by adding a new brain region. Finally, we will save it as a *.atlas file.

1. Select File $\to$ Import (xls) and select your file as shown in figure 2. After you select the file, the table and the brain surface are updated to show the brain atlas.

Figure 2: Importing a brain atlas saved as an Excel file into GUIBrainAtlas.

2. As shown in figure 3, a region can be selected by clicking on its checkbox on the left side of the table. A selected region appears red on the brain surface. Alternatively, right-click on the desired region on the brain surface and push Select on the popup menu; if a region is already selected, then Deselect appears on the popup menu.

Figure 3: Brain regions can be selected by clicking on the corresponding checkbox or by right-clicking on the desired region on the brain surface. When selected, they appear red on the brain surface.

3.  Push Add at the bottom of the table to add a new brain region. A default region is added with label BR’, name br name’, and coordinates $(0,0,0)$ — see brain region 69 in figure 4. You can now edit these properties by clicking on them in the table. This new brain region has been added at the end of the table; to add it at a different position in the table, select a brain region and push Add below or Add above.

Figure 4: Adding a new brain region to a brain atlas.

A series of options is available to edit and modify the brain atlas. These are accessible both through the buttons at the bottom of the table and through the menu on the top of the interface. These are:

• Select all selects all the brain regions.
• Clear selection clears the current selection.
• Add adds a brain region at the end of the table.
• Remove removes the selected brain regions.
• Move up moves the selected brain regions up by one place.
• Move down moves the selected brain regions down by one place.
• Move to top moves the selected brain regions to the top of the table.
• Move to bottom moves the selected brain regions to the bottom of the table.
4. Push 3D in the brain view to change the visualization of the brain atlas on the brain surface, as shown in figure 5. By selecting Brain View $\to$ Generate figure, the brain view can be exported as a MatLab figure; the same can be achieved with Ctrl+F.

Figure 5: Changing visualization of the brain and exporting a 3D view of the brain to a MatLab figure.

5. Select File $\to$ Save to save the brain atlas as a *.atlas file; alternatively you can also use the shortcut Ctrl+S or the Save icon on the toolbar.
6. Select File $\to$ Open to open a brain atlas previously saved with GUIBrainAtlas; alternatively you can also use the shortcut Ctrl+O or the Open icon on the toolbar.

File formats that can be imported

A brain atlas can be imported from Excel (*.xls or *.xlsx), text (*.txt), or xml (*.xml) files only if these files are in the correct format. For examples, see the files desikan_atlas.xlsx, desikan_atlas.txt, and desikan_atlas.xml.

In order to be imported correctly the Excel file should have the format shown in figure 6. It must include only one sheet. The first row must include the metainformation about the brain atlas, i.e. the atlas name (A1) and the atlas surface (B1). Each of the following rows (e.g. row 2) must contain the information relative to a brain region, including code (e.g. A2), name (e.g. B2), x-coordinate (e.g. C2), y-coordinate (e.g. D2), z-coordinate (e.g. E2), hemisphere (left’ or right’, e.g. F2), and notes (e.g. G2). Importantly, the note column must contain some values (in our sample file we just added ‘.’).

Figure 6: Format of the Excel file containing a brain atlas required to be imported correctly.

The format for the text file is essentially the same, including a first row with the name and brain surface, and the following rows with the information about the brain regions (see desikan_atlas.txt).

The xml format is slightly more complex, but can be easily inferred from the sample file desikan_atlas.xml.

Brain View

The brain view permits one to visualize the brain regions on top of a brain surface based on the ICBM152 template.[2] The brain surface can be visualized in different ways by using the buttons below the brain view:

• 3D
• Sagittal left
• Sagittal right
• Axial dorsal
• Axial ventral
• Coronal anterior
• Coronal posterior

The slider adjusts the transparency of the brain. The checkboxes are used to turn on and off the brain surface (Show brain), the axis (Show axis), the grid (Show grid), the brain regions (Show brain regions), and the labels (Show labels). To visualize the information about a brain region (i.e. label, name, position, hemisphere, and notes), right-click on it, and push Info on the popup menu.

File provides various options for importing and saving a brain atlas:

• File $\to$ Open} (Ctrl+O) opens a popup window to load an atlas saved in *.atlas format.
• File $\to$ Close (Ctrl+C) closes the GUIBrainAtlas.
• File $\to$ Save (Ctrl+S) saves the current atlas in *.atlas format.
• File $\to$ Save as} opens a popup window to save the current atlas in *.atlas format possibly in a different file.
• File $\to$ Import (xml) imports an atlas from an xml file.
• File $\to$ Import (txt) imports an atlas from a text file.
• File $\to$ Import (xls) imports an atlas from an Excel file.
• File $\to$ Export (xml) exports the current atlas to an xml file.
• File $latex\to$ Export (txt) exports the current atlas to a text file.

Edit provides various options to edit or change brain regions:

• Edit $\to$ Select all selects all the brain regions.
• Edit $\to$ Clear selection clears the current selection.
• Edit $\to$ Add (Ctrl+A) adds a brain region at the end of the table.
• Edit $\to$ Add above adds brain regions above the selected ones.
• Edit $\to$ Add below adds brain regions below the selected ones.
• Edit $\to$ Remove (Ctrl+R) removes the selected brain regions.
• Edit $\to$ Move up (Ctrl+U) moves selected brain regions up by one place.
• Edit $\to$ Move down (Ctrl+D) moves selected brain regions down by one place.
• Edit $\to$ Move to top (Ctrl+T) moves selected brain regions to the top of the table.
• Edit $\to$ Move to bottom (Ctrl+B) moves selected brain regions to the bottom of the table.

Brain View $\to$ Generate figure (Ctrl+F) generates a figure that can be customized using the standard MatLab plotting tools. The figure can then be exported in several standard graphic formats.

Subject Cohorts provides a series of options to launch the cohort manager programs for various imaging modalities using the current brain atlas:

• Subject Cohorts $\to$ MRI Cohort launches GUIMRICohort.
• Subject Cohorts $\to$ fMRI Cohort launches GUIfMRICohort.
• Subject Cohorts $\to$ PET Cohort launches GUIPETCohort.
• Subject Cohorts $\to$ EEG Cohort launches GUIEEGCohort.

About $\to$ About provides information about the current version of GUIBrainAtlas and BRAPH.

Toolbar

The toolbar provides different options to open, save, and visualize the brain surface. It is shown in figure 7.

Figure 7: GUIBrainAtlas toolbar.

Open and save commands
These commands allow the user to open and save a brain atlas in the *.atlas format. These are equivalent to the open and save menu options in the File menu.

opens a popup window to load an atlas saved in *.atlas format.

saves the current atlas in *.atlas format.

Visualization commands
zooms in brain view.
zooms out brain view.
drags brain view.
rotates brain view
shows/hides data cursor.
standard 3D view.
sagittal left view.
sagittal right view.
axial dorsal view.
axial ventral view.
coronal anterior view.
coronal posterior view.
switches brain surface on/off.
switches axis on/off.
switches grid on/off.
switches brain regions on/off.
switches brain region labels on/off.

Watch also:

Brain Atlas

Footnotes and references

1. ^ Desikan, Rahul S., et al. “An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.” Neuroimage 31.3 (2006): 968-980.
2. ^ Mazziotta, John C., et al. “A probabilistic atlas of the human brain: Theory and rationale for its development: The international consortium for brain mapping (icbm).” Neuroimage 2.2 (1995): 89-101.