[Brains-users] Some questions regarding segmentation

[Ronald Pierson]

I suggest you take some time to go through the Standard Workup manual
that can be found on the WIKI page of our web site.

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

BRAINS does a full workup, including creation of a fantastic mask of the
brain.  We don't call it skull stripping, it really is more focused on
careful definition of brain and CSF.

Standard workup is normally done with a T1 and T2, with addition of a PD
if it is available.  A T1-only classified image is really not the best,
no matter what package is used to create it.

A quick summary of our workup - 

1. The first step is to realign the T1 (AC-PC), pick Talairach
parameters, then coregister the T2 to the T1 (using alignlinear or
mutual information coregistration from the toolbar).  

2. Then, blood is traced.  Tissue classification (we also call this step
segmentation) is completed using both a T1 and T2 so that there is a
very clear definition of brain vs nonbrain.  If you us only a T1-like
image, you will need to use a different designation for blood, maybe the
250 voxels from the top of the image (outside of the image space).  That
is because blood is very similar in intensity to gray matter on a T1,
and you can't make any distinction to discriminate between blood and
gray matter without more information from the T2.

3.  At that point, and actually as part of tissue classification, a mask
is generated that is analogous to what you refer to as skull stripping.
We go the extra step to manually edit this brain mask before measuring
brain volumes.  We really feel that this brain mask is far superior to
anything else currently available.

FYI - we actually don't like the use of basal gray and basal white any
more.  There really is too much variability between traces in what gets
picked.

Ronald Pierson


-----Original Message-----
From: brains-users-bounces at psychiatry.uiowa.edu
[mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of
Christoph Christmann
Sent: Tuesday, January 24, 2006 3:02 AM
To: brains-users at psychiatry.uiowa.edu
Subject: [Brains-users] Some questions regarding segmentation

Hi all,

At first I am facing a serious problem during the segmentation. I did 
skullstrip, import, resample, crop and lighten up a FLASH image. Then 
I created a mask of the brain (with image tools - threshold) the 
Talairach parameters, and sampled ROIs for venous blood and basal 
white and grey matter. Images, ROIs and masks show up in the 
segmentation dialogs (i.e. no appearance of a '-1'). However, after 
running segmentation (without BOOTSTRAP) the tissue qualification 
seems shifted, for example white matter will completely be qualified 
as grey matter. Has anyone an idea what's inducing this behaviour and 
how this can be fixed?

A second question is concerning the skull stripping. Is there any 
tool apart from MRIcro that could be used effectivly to separate the
brain?

The last question applies for the use of T2 images. While it seems 
quite reasonable to integrate the T2 images for the ROI analysis I 
wonder if the T2 image is used for the segmentation of the T1 image.

Thanks in advance for any hint!

Christoph





-- 
Christoph Christmann                  christma at as200.zi-mannheim.de
Psychologist, MEE                     Fon/Fax +49 621 1703 63 18/05
Central Institute of Mental Health    http://www.zi-mannheim.de
Department of Neuropsychology         D-68159 Mannheim J5
and Clinical Psychology                

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