[Brains-users] Tissue Classification

[Hans Johnson]

http://www.psychiatry.uiowa.edu/wiki/index.php?title=BRAINS_FAQ

Tissue Classification
PROBLEM: (from David L. Dean on 4-25-2005)
We've been working with Brains2 for about 6 months now, and we've had a good
amount of success with performing the standard workup on over 200 of our
scans. We're able to get whole tissue and segmented lobar volumes, and we're
now looking to do more ROI tracing and the surface data. However, we wanted
to ask you about a particular problem that we have with the tissue
classification step.
Given that we are working with Alzheimer's and dementia patients, we have
found that many of our patients have a significant amount of white matter
disease, which results in the white matter being misclassified as grey
matter. When I examine the standard workups that we've done, it appears that
about half of the scans have a significant amount of white matter being
misclassified in this way.
And so our first question is whether or not this is something that you deal
with at the IPL? And if you do, how do you go about excluding or fixing
those scans with a noticable amount of white matter disease?

ANSWER: (from Vincent Magnotta) We have done some imaging in an elderly
sample and have seen similar problems on certain scans. There are really two
answers to your question.
If the problems that you are referring to are not the result of white matter
hyperintensities (WMH) then the problem can usually be fixed by changing the
plug picking parameters. Often you can simply iterate through the plug
picking step and use the plugs as a guide to the quality of the
segmentation. If I remember correctly, we often lowered the number of plugs
required and this fixed many of the scans. These are only general statements
since I have not seen the images.
If the problems result from a large number of WMH then there is not an
immediate solution. I am looking at a sample of scans this week that have
WMH and we are investigating how these data should be handled.
If you would like to send a scan, we can look at it and provide some more
specific feedback.