In this third example, we will compute magnetisation transfer
ratio (MTR) images, and whole-brain MTR histograms.
For this measurement we will use a pair of images: one without
off-resonance saturation pulses, and one where these pulses are
included. The first image is normally a regular
proton-density-weighted image that may be acquired using a
spin-echo or gradient-echo sequence. The second image is acquired
in an identical way to the first, except that it includes
additional off-resonance RF saturation pulses that affect the
longitudinal magnetisation of protons in the larger molecules,
such as cell membranes. These two images will be referred to as
M0
and Ms
respectively.
The analysis comes in three stages:
M0
image.
M0
and Ms
images
need to be in two separate UNC, Analyze or NIFTI image files before
analysis starts. Use the image
converter to create these two images. If your pulses sequence
puts the two images into one image file, use the Slice Extractor tool to
separate them out into two image files. The two images must have
the same number of rows, columns and slices.
Below is an example of a proton-density image before and after removal of extra-cerebral tissue.
Before extra-cerebral tissue removal.
After extra-cerebral tissue removal.
Save the edited proton-density image to a new file.
Bring up the image statistics dialog to show the histogram of pixel intensities. Many images have a large number of pixels with zero intensity: ensure that you have the check-box selected in the image statistics dialog, which will remove the large histogram peak at zero intensity. The image statistics window will now show the image intensity histogram:
The peak to the left is from pixels outside the head that contain just noise. Choose an intensity threshold so that most of pixels that contain just noise are below the threshold. In the example above, you can see that a threshold of about 100 would remove the peak to the left. The choice is not critical, but do not choose too high a threshold, or pixels containing tissue of interest may be removed.Threshold
field.
Presets
menu, select Magnetization
Transfer Ratio (MTR) (0.1% bins)
. The MTR
calculation will produce an image with intensities between 0 and
1000 (note the scaling factor of 1000 in the formula). 0
corresponds to 0% MTR, and 1000 corresponds to 100% MTR. Thus, changes of
1 intensity unit correspond to changes of 0.1% in MTR.Presets
menu, select Magnetization
Transfer Ratio (MTR) (1% bins)
. The MTR
calculation will produce an image with intensities between 0 and
100 (note the scaling factor of 100 in the formula). 0
corresponds to 0% MTR, and 100 corresponds to 100% MTR. Thus, changes of
1 intensity unit correspond to changes of 1% in MTR. This larger bin width
will help to smooth the histogram.Input Images
panel by
clicking on the icon. Note that first image is
the proton-density image (M0
) and the second is the image with
saturation pulses (Ms
). Click on the
button to start the MTR calculation.
If you want to save the MTR image, select this from the option
in the Algebra Frame.
However, you can always save the
result later from the File
menu of Jim's display.
File
menu,
choose Write
: . A File Chooser now pops up prompting
you for a file name to save the histogram.