Atlases¶
FSL comes bundled with a collection of NIFTI templates and atlases. A variety of probabilistic and discrete atlases are included, comprising cortical, sub-cortical, and regional parcellations. It is also possible to add your own atlases to FSL.
The atlas panel, available in Orthographic and lightbox views, allows you to browse and search through these atlases. An atlas panel can be added to a view via its settings menu, e.g. Settings ⇒ Ortho view 1 ⇒ Atlas panel.
The atlas panel is organised into three main sections - Atlas information, Atlas search, and Atlas management. These sections are accessed by clicking on the tabs at the top of the panel.
Atlas information¶
The atlas information tab displays information about the current display location, relative to one or more atlases:
The list on the left allows you to select the atlases that you wish to query - click the check boxes to the left of an atlas to toggle information on and off for that atlas. The Harvard-Oxford cortical and sub-cortical structural atlases are both selected by default.
The panel on the right displays information about the current display location from each selected atlas. For probabilistic atlases, the region(s) corresponding to the display location are listed, along with their probabilities. For discrete atlases, the region at the current location is listed.
You may click on the Show/Hide links alongside each atlas and region name to toggle corresponding image overlays on and off.
- For atlases, the Show/Hide link toggles a discrete label overlay.
- For regions from a discrete label atlas, the Show/Hide link toggles a discrete mask overlay which just contains the voxels in that region.
- For regions from a probabilistic atlas, the Show/Hide link toggles a probabilistic volume overlay, containing the probabilistic map for that region.
Atlas search¶
The atlas search tab allows you to browse through the atlases, and search for specific regions.
The list on the left displays all available atlases - the checkbox to the left of each atlas toggles a label overlay for that atlas on and off.
When you select an atlas in this list, all of the regions in that atlas are listed in the area to the right. Again, the checkbox to the left of each region name toggles an overlay for that region on and off (either a volume or mask overlay, depending on whether the atlas is probabilstic or discrete). The + button next to each region moves the display location to the (approximate) centre of that region.
Searching for regions¶
The search field at the top of the region list allows you to filter the regions that are displayed.
When you type some characters into the search field, the region list will be filtered, so that only those regions with a name that contains the characters you entered are displayed. The atlas list on the left will also be updated so that any atlases which contain regions matching the search term are highlighted in bold.
Atlas management¶
The atlas management tab displays a list of all loaded atlases, and allows you to add and remove atlases from FSLeyes. The name of each atlas is shown in the list, but you can click and hold on an atlas to display the path to the atlas specification file.
You can load a new atlas into FSLeyes by clicking the + button, and selecting the FSL atlas specification file which describes the atlas - see the page on customising FSLeyes for details. You can remove an atlas from FSLeyes by selecting it in the list and clicking the - button [*].
| [*] | If you remove an atlas that is located in $FSLDIR/data/atlases/ it
will be re-loaded the next time you start FSLeyes. |