Quick start¶
Help!¶
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 File
⇒ Add 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
button will open a dialog containing all of the overlay display
settings. Pushing the
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 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 Settings ⇒ Ortho view 1 ⇒ Atlas 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 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
button).
View images in neurological/radiological orientation?¶
You can switch between a radiological or neurological display, in the
view settings panel (the
button).
Take a screenshot?¶
Click the button on the ortho toolbar, or select the Settings
⇒ Ortho view 1 ⇒ Take screenshot menu item.
Link/unlink the display properties across multiple views?¶
If you have more than one view open (e.g. an ortho view and a lightbox view), and you want the overlay display settings to be the same across all views, make sure that the Settings ⇒ <view name> ⇒ Link display settings menu option for all views is selected.
This setting is also available via the view settings panel (via the toolbar button,
or the Settings ⇒ <view name> ⇒ View settings
panel menu option), as the Link overlay display settings check box.
Link/unlink the volumes on two or more 4D images?¶
If you want to view the same volumes from two or more 4D NIFTI images, make
sure the button, in the overlay list, is enabled for each image.
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 () 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 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 Settings ⇒ Ortho view ⇒ Edit 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 View ⇒ Layouts
⇒ MELODIC 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 View ⇒ Layouts ⇒ Save current layout menu item, and give your layout a name. You can then restore it at any time by selecting it in the View ⇒ Layouts menu.