FSLView - User GuideFSLView Version 1.0 | ![]() |
FSLView is a simple viewer for 3D and 4D 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:
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:
i
button and change the image's
colour display scheme (LUT - look-up-table), and see some basic image
information
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
.