Brain Finder - Outlining The Brain
The first stage towards measuring brain atrophy is to isolate the
brain from the surrounding tissue, such as subcutaneous fat, eyes
muscle etc. This stage can either be done automatically (with
manual editing if necessary) using the "Find Brain" function, or
manually by contouring the outline of the brain on each slice.
In either case, the result will be a set of ROIs - one (or possibly
more that one) in every slice that define the outer boundaries of the brain.
Load an image containing an MRI head scan covering the whole
brain. This could be:
- Multi-slice T1-weighted.
- Multi-slice FLAIR.
- 3-dimensional acquisition T1-weighted.
You could also use the Brain Finder to isolate the brain on
T2-weighted images, although you could not then go on
to measure the atrophy.
The following options need to be chosen:
- Uniformity correction.
It is strongly recommended that intensity uniformity correction is
performed as part of the brain finding procedure, since this
vastly improves the scan-rescan reproducibility. However,
uniformity correction is quite time-consuming (1-2 minutes), and
you may want to turn it off for when not performing a detailed
study using the
check
box. Uniformity correction is an iterative procedure, and the
maximum number of iterations allowed is set in the text box to the
side: 
. In the
unlikely event that the uniformity correction procedure fails with
a message that the maximum number of iterations was exceeded, you
may wish to increase the value from its default of 2000 iterations.
- Odd-even slice correction.
If you are working with multi-slice MR images (not 3D FLASH images),
you may also find it advantageous to select the
check-box. This will correct that slice
differences in intensity that are found in multi-slice images acquired in
an "interleaved" fashion.
- Threshold fraction.
Brain Finder has one adjustable parameter that can be altered by
the user to improve the resulting brain outline, the "threshold fraction" (default
value 0.5). Brain Finder is
pre-configured with a setting that works well with most MRI scans of
the head, and the Clicking on the
button puts the settings back to its
default value.
The parameter acts as follows:
- The surface of the brain is found
at the intensity threshold between the interior of the brain and
the background signal in the skull. A low setting of this
threshold will push the brain outline further towards the skull,
and a higher setting will pull the brain outline inwards. In FLAIR
images, where the patient has a lot of hyperintensities, the mean
intensity in the brain is much higher than at the cortical
surface, and thus the intensity threshold will also be higher (for
a fixed value of the threshold fraction). In FLAIR images it may
be necessary to use a lower setting of the threshold fraction
(e.g. 0.3 - 0.4).
Note: whatever setting you use for your images, for both
cross-sectional and serial studies it is important to maintain the
same settings for all patients scanned on any given
scanner. Because of differences in contrast from scanner to
scanner, it may be necessary to adjust the setting on a
scanner-by-scanner basis, but for serial studies it is imperative
that the same settings are always used for any given patient.
- Enhanced brain extraction.
There may be errors in the brain outline that the Brain Finder tool
finds, particularly around in the region of the eyes and around blood
vessels. These tissues are often bright on T1-weighted
images, particularly 2-D spin-echo images, and this option can help to
remove some of the erroneous tissues.
"Enhanced" option for brain extraction.
 |
| Not enhanced. |
 |
| Enhanced extraction. |
Enhanced brain extraction works by identifying those tissue which are
very much brighter (greater than 2.5 standard deviations from the mean)
than the average brain intensity.
Note: enhanced brain extraction takes quite a long time.
- Orientation.
The orientation of the slices acquired (axial, coronal, sagittal) does not
matter; however, if the orientation is coronal or sagittal then
click on:
This makes Brain Finder more reliable by initialising the search
for the brain away from the neck, which is prominent in sagittal
and coronal images.
- Write to VRML file.
The Brain Finder will create ROIs surrounding the brain.
However, you may want to visualise the brain surface in
Jim's 3-dimensional display. If you
select the
check box,
then a surface model of the brain will be created, which can then
be loaded into the 3-D Display as a virtual reality modelling
language (VRML) file. The VRML file created will have a name taken from
the input image name, with an extension .wrl.
Next, click on the 
button. This
starts the uniformity correction (if selected) followed by an iterative
search for the brain outline. During the search, a
progress monitor pops up, which can be cancelled at any time:
During the brain finding operation, the ROI toolkit is disabled.
When the brain has been found, ROIs are created that define the
outline of the brain, and a message pops up:
You now have a chance to review the brain outline found, and to
edit the ROIs if you are not happy with Brain Finder's
results. Click "OK" to acknowledge the message.
In some image slices, the brain may appear as multiple regions of
interest. When editing the regions, you should retain all ROIs
that actually contain brain parenchyma. In other slices, ROIs may
have other ROIs within them, as in the example below:
This happens when the surface of the brain is concave; the
internal ROI will not be counted as part of the brain.
You should now edit the
ROIs if necessary, to correct the brain outlines found
automatically. If you prefer, you can define the ROIs in every
slice by manually outlining
the brain, or by using ROI
contouring. When you are happy with the ROIs in every slice,
then proceed with calculating the BPF.
Note: you should save the ROIs as a
permanent record of the brain outline found.