[Brains-users] FW: Brains2 Tissue Classification -- White Matter Disease

[Hans Johnson]

------ Forwarded Message
From: "Dean, David" <ddean at memory.ucsf.edu>
Date: Tue, 26 Apr 2005 12:20:02 -0700
To: <vincent-magnotta at uiowa.edu>
Cc: Hans Johnson <hans-johnson at uiowa.edu>, "Rosen, Howie"
<hrosen at memory.ucsf.edu>
Subject: RE: Brains2 Tissue Classification -- White Matter Disease

Thanks Dr. Magnotta.

Yes, I've tried playing with the input parameters to the segmentation
algorithm, and we've had some success.  We've been able to fix some
segmentations that initially appeared whited out, or the csf appeared
cloudy, primarily by reducing the grey matter plugs from 4000 to 2000,
as well as by increasing the 'permissiveness' from 0.10 to 0.30 and
reducing the 'trim mean outlier' from 2.5 to 1.5.

What are the default input parameters that you are currently using for
your standard workup?

Also, if we wanted to send you some examples of some our our workups, is
there an easy, secure and legal way to do that?

Thanks a bunch, and good luck with everything at the IPL.
David

-----Original Message-----
From: Vincent A. Magnotta [mailto:vincent-magnotta at uiowa.edu]
Sent: Monday, April 25, 2005 3:59 PM
To: Dean, David
Cc: Hans Johnson; Rosen, Howie
Subject: Re: Brains2 Tissue Classification -- White Matter Disease


David,

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.

Vince


On Mon, 2005-04-25 at 17:18, Dean, David wrote:
> Hi Drs. Johnson and Magnotta,
> 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?
> Thanks,
> David
> 
> David L Dean
> Brain Image Analysis Coordinator
> UCSF Memory and Aging Center
> 350 Parnassus, Suite 706
> San Francisco, CA 94143-1207
> http://www.memory.ucsf.edu/
> 
> Phone: 415-502-0619
> Fax: 415-476-0213
> ddean at memory.ucsf.edu
-- 
Assistant Professor
Department of Radiology
0453-D JCP
200 Hawkins Drive
Iowa City, IA 52242
E-mail: vincent-magnotta at uiowa.edu
Phone: 319-356-8255
Fax: 319-353-6275
Website: http://www.radiology.uiowa.edu



------ End of Forwarded Message