Overview¶
FSLeyes is a viewer for 3D and 4D neuroimaging data. It is intended as a replacement for the much loved FSLView. FSLeyes offers similar functionality to FSLView, and aims to improve and expand upon this functionality in many ways.
Overlays¶
FSLeyes refers to the files that you load as overlays. Where FSLView referred to files as images, FSLeyes uses the term overlay because FSLeyes is capable of displaying more than just NIFTI images [*]. These files can be displayed in a variety of different ways - see the page on overlays for more information.
[*] | FSLeyes 0.32.0 is able to load NIFTI, MGH, GIFTI, Freesurfer, and VTK files. Future versions of FSLeyes will be able to load more file types. |
Within a FSLeyes view, you can tell which overlay is selected by looking at the name field on the overlay display toolbar, or looking at the highlighted item in the overlay list. Many operations in FSLeyes will be applied to the currently selected overlay, such as adjusting the overlay visibility, brightness and colour map.
The Overlay menu contains options for changing the selected overlay, and performing some operations on the currently selected overlay:

The display space¶
FSLeyes works under the assumption that all of the overlays you load are defined in the same space. For example, if you load a T1 image and a T2* image, FSLeyes will attempt to display them on top of one another, even if they have different resolution or orientation. By default, FSLeyes will display all overlays in terms of a single reference overlay, typically the first one that you load. The reference overlay is displayed so that it is orthogonal to the display coordinate system; all other overlays are transformed into the space of this reference overlay. You can change the reference overlay via the Display space option in the view settings panel.
If you are having trouble with mis-aligned images, or are interested in how FSLeyes works, refer to the page on the display space.
Views and controls¶
The FSLeyes interface is arranged into views and controls.
Conceptually, a view (e.g. an orthographic or time series panel) displays the data in some way, and a control (e.g. an overlay display toolbar or atlas panel) allows you to manipulate that view. Views are top-level panels, whereas controls are embedded within a single view.
All available views are listed in the View menu:

When you open a new view, a sub-menu for that view is added to the Settings menu. This sub-menu contains some actions that can be executed on the view, and also contains a list of all the controls which can be added to the view. For example, the settings menu for an orthographic view looks like this:

Views and controls are described in more detail in the pages on orthographic/lightbox views, plotting views, and the 3D view.
Tools¶
Under the Tools menu, you can find a set of options which allow you to perform various actions, typically affecting the currently selected overlay. Some tools are always present, whereas others are associated with a specific view, and will only be present if you have one of those views open.
More information on the FSLeyes tools can be found on the tools page.
Layouts¶
FSLeyes allows you to lay out your view and control panels in any way you like.
Whenever you have more than one view open, you can re-arrange them by clicking and dragging their title bars, and dropping them onto the docking icons which appear. You can also re-arrange the control panels within a view in the same way. These docking icons, shown below, will appear on the FSLeyes frame whenever you click and drag the title bar of a view or control panel:





FSLeyes refers to a specific view and control panel arrangement as a layout. If you have a layout which you like, or use frequently, you can save it, and restore it later on. All of the options for managing layouts can be found in the View ⇒ layouts sub-menu:

Built-in layouts¶
FSLeyes comes with a few built-in layouts, described below.
Default layout¶
This is the default FSLeyes layout, inspired by FSLView, and useful for general image viewing and editing.

MELODIC mode¶
This layout is designed to assist in manual classification of ICA components. It provides functionality similar to that of the Melview tool, comprising a lightbox view and plot panels which display the time course and power spectrum of the currently selected component. A classification panel allows you to load, save, and edit the classification labels for each component. See the page on IC classification for more information.

FEAT mode¶
This layout is designed to assist in exploring the results of a FEAT analysis. The cluster panel displays a table of clusters for each contrast (for analyses which used cluster thresholding), and the time series panel allows you to view full and partial model fits to the data. See the page on viewing FEAT analyses for more information.

Plain orthographic/lightbox/3D¶
These layouts simply display a plain orthographic, lightbox, or 3D view, respectively.