FSLView - User Guide

FSLView Version 1.0

INTRODUCTION

FSLView is a simple viewer for 3D and 4D data:

"ortho" (3 orthogonal slicings) and "lightbox" (mutiple slices) view options
multiple simultaneous views (ortho and/or lightbox)
time-series display (via graphs or movie loops)
multiple semi-transparent colour-overlays
simple freehand image editing (mask drawing)

FSLView uses some new features of OpenGL which are not yet present on all hardware. In particular, lightbox view mode and variable transparency in colour overlays may not be functional on some computers.

Quick Introducion to FSLView

Find and uncompress the example data

cd ~{FSLDIR}/doc/fslview/data gunzip *

Start FSLView by typing

fslview &

Load in the image example_func.hdr, by pressing
File -> Open

Hold the mouse button down in one of the view panels and move it around - see how various things update as you do so:

the other panels update their view
the cursor's position in both voxel and mm co-ordinates gets updated
the image intensity at the cursor is shown

Now click several times on the (very) small "+" by the scale control (currently showing "100%"). This is one way of controlling the zoom. If you click on the icon of a hand you can drag a view around. You can reset the view settings by pressing on the button with the two small concentric circles. You can also set the field-of-view of a panel by clicking on the button with two small squares, and click-and-dragging the mouse in a view panel.

Return to "normal view mode" by clicking on the button with the small cross. You can turn the crosshairs on and off with the small checkbox (white box with/without tick) nearby.

You can control the brightness and contrast either by using the relevant sliders, or by typing numbers into the nearby boxes. Press either of the small brightness/contrast buttons to reset the settings.

Now load in a second image (over the current image of example_func.hdr) using File -> Add; thresh_zstat1 is a thresholded FMRI stats image. In the bottom-left panel is a list of loaded images. At the bottom of the list is the "primary" loaded image which is always underneath all others. Images can be turned on and off by double-clicking; also, once highlighted, an image's transparency can be changed with the slider (at the bottom of the box); reduce the "solidity" of the stats overlay image.

Also, when an image in the image list is highlighted:

you can click on the i button and change the image's colour display scheme (LUT - look-up-table), and see some basic image information
you can set the brightness/contrast settings for that image, as described above
you can view voxel intensities for that image in the normal place (to the right of the voxel co-ordinate displays)

Now close down all views; all loaded images have now been deleted from FSLView. Now load in filtered_func_data, a 4D FMRI time series. Now watch this as a movie by pressing the film-strip button that appears when a 4D file is loaded as the "primary image"; you will see the time-counter display scrolling through the different time-point values. Note that whilst the movie is running you can still change the cursor position. You can even re-load the thresh_zstat1 stats overlay image back in whilst the movie is running. Stop the movie by pressing the movie button again.

Open a timeseries graph view with View -> Timeseries. Move around with the cursor until you are on a "highly activated" voxel. Press the + button in the timeseries view and you will see the timeseries graph for that voxel; you should be able to see the boxcar paradigm reflected in the data. You can add more timeseries by moving to new voxels and pressing + again.

To view a basic histogram of the currently displayed image press View -> Image histogram. A histogram is nothing more than a plot of the distribution of intensities in the image - image intensity is on the x axis and the number of voxels with that intensity is on the y axis.

To create a hand-drawn mask first load an image, then press File->Create Mask. Switch to mask-drawing mode by pressing the pencil icon. (Note - you can draw in any image by also unlocking the relevant lock icon in the image list.) When you enter mask-drawing mode you will see the mask-drawing toolbar become enabled. The left value-box controls the value that will be written into the mask image when you mouse-left-click in the image; the right value-box controls the pen size. You can undo work with the right-most undo icon. To zero (remove) set voxels, simply change the left value-box to zero. Once you have finished editing a mask you can save to file with File->Save as.