What you are suggesting all sounds sensible.
The one thing that might prove tricky is the skull estimation.
You need to avoid there being an "edge" of intensity change
right at the brain edge, or otherwise it won't find the skull and
will be normalising to the brain size, which is not what you
want for determining atrophy.
So try just subtracting a proportion of the brain from the
original image, just to dark this boundary but leave the skull/scalp
boundary as a stronger one. Try that and run BET on it and see
if you are getting a decent result for the skull/scalp points. Note
that they are never perfect but as long as over half are on the
correct surface then things should work OK. The best way of
telling whether it is working well is to look at the registration outputs
and check that the skull/scalp is well aligned. If not, then it will
still require some fixing.
I hope this helps.
All the best,
On 22 Sep 2011, at 22:28, Martin M Monti wrote:
> Hi, I am working with sienax to get some volumetric info on a group of patients, but the brains are so pathological that automatic bet and registration are really thrown off. Indeed, for many of these patients I had to manually go in and delete bits of skull/eyeballs/neck that I just can't seem to remove with bet.
> Now, I do have (manually adjusted) brain extracted images for each of these patients, so I am trying to see if I can use them to work-aroud the sienax script. This would require 2 things:
> 1) generate a skull image (which unfortunately I do not have..). Is there a way I could generate them from the bet-ted brain (e.g. if I subtracted the bet-ted brain from the original image, would that be usable for the purposes of sienax as a *_skull.nii.gz image)?
> 2) Once I have _brain and _skull images I should be able to comment out the bet command in the sienax script and run it from there?
> Does it sound possible? Is there a better/different way to work with these "unbettable" brains?
> Martin M Monti, PhD
> Assistant Professor
> 7461E Franz Hall
> UCLA Department of Psychology
> BOX 951563,
> Los Angeles, CA 90095-1563
> http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3 <http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3%20>
> “Well! I’ve often seen a cat without a grin,” thought Alice,
> “but a grin without a cat! It’s the most curious thing I ever
> saw in my life!” [Lewis Carroll, Alice in Wonderland]