Quick start


If you get stuck:

  • Search through these help pages to see if your problem is discussed anywhere.

  • If you can’t figure out how to do something, see if it is covered in the How do i … section, below.

  • If something has gone wrong, check the Troubleshooting page to see if you problem is covered there.

Most FSLeyes buttons and controls also have tooltips which contain useful information, and which will pop up if your hover the mouse over a control for a couple of seconds:


The interface

When you first start FSLeyes, you will be presented with something that looks like this:


This is slightly boring, so let’s load an image. Select the FileAdd from file menu option, and choose a .nii.gz image to load.

Now things are a bit more interesting:


Let’s take a closer look at the components of the FSLeyes interface…


The view

The view is where your overlays are displayed. By default, an orthographic view is shown; you can also select a lightbox view, a 3D view, or some plot views, from the View menu.

Let’s stick with the orthographic view for now. It displays your overlay on three canvases, along the three primary axes. For a NIFTI image which is oriented acording to the MNI152 template, these canvases will correspond to the sagittal, coronal, and axial planes.

You can interact with an ortho view in a number of ways. Use the mouse to click, or click and drag, to change the current location. Hold down the ⌘ key (OSX) or ⌃ key (Linux), and use your mouse wheel to zoom in and out of a canvas. You can also middle-click and drag, or hold down the ⌥ key and drag with the left mouse button, to pan around.

See the section on ortho view interaction for more hints on working with an ortho view.

The overlay list

The overlay list displays a list of all overlays that you have loaded. Amongst other things, this list allows you to add and remove overlays, toggle overlay visibility, and change the overlay display order.

The location panel

The location panel shows the current display location, in terms of the currently selected overlay. It also shows the overlay data value at the current location, for every loaded overlay.

The toolbars

The overlay toolbar allows you to adjust display properties of the currently selected overlay. Pushing the gear_icon button will open a dialog containing all of the overlay display settings. Pushing the information_icon button opens a dialog containing information about the overlay.

The ortho toolbar allows you to adjust the layout of the ortho view. For example, you can toggle each of the canvases on and off, and switch between vertical, horizontal, or grid layouts. Pushing the spanner_icon button will open a dialog containing all of the ortho view settings.

How do I …

Load an overlay?

See Loading an overlay.

Open another ortho/lightbox view?

The View menu allows you to open another view. You can open as many views as you like.

Open/close control panels/toolbars?

The Settings menu contains a sub-menu for every open view, which allows you to toggle the control panels and toolbars for that view, and perform a few other tasks. For example, if you want to add an atlas panel, you would select the SettingsOrtho view 1Atlas panel menu option. See Views and controls for more information.

Change the background colour?

You can change the background and cursor colours via the view settings panel (the spanner_icon button on the ortho toolbar).

Show/hide the cursor/anatomical labels?

You can toggle the cursor and labels simultaneously via the + button on the ortho toolbar, or toggle them independently via checkboxes in the view settings panel (the spanner_icon button).

View images in neurological/radiological orientation?

You can switch between a radiological or neurological display, in the view settings panel (the spanner_icon button).

Take a screenshot?

Click the camera_icon button on the ortho toolbar, or select the SettingsOrtho view 1Take screenshot menu item.

Set up a positive/negative colour map for Z statistics?

You can set up a negative colour map by clicking on the negative colour map button (posneg_cmap_icon) on the overlay display toolbar. The top colour map on the toolbar will be used for positive values, and the bottom colour map for negative values.

You can also set up a negative colour map through the overlay display panel (the gear_icon button on the overlay display toolbar). See the section on volume display settings for more details.

Edit a NIFTI image?

You can edit NIFTI image data from within an orthographic view. Switch to edit mode via the SettingsOrtho viewEdit mode menu option. This will open a new toolbar which contains editing functionality. See the page on editing images for more details.

Classify ICA components?

Load your .ica directory (or the .ica/melodic_IC image file), then open the melodic layout (the ViewLayoutsMELODIC mode menu option). See IC classification for more information.

Save the current view/control panel layout?

You can save a layout at any time: Choose the ViewLayoutsSave current layout menu item, and give your layout a name. You can then restore it at any time by selecting it in the ViewLayouts menu.