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. SettingsOrtho view 1Atlas 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:

_images/atlases_atlas_information.png

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 management

_images/atlases_atlas_management.png

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.