[Brains-users] Some questions regarding segmentation

[Eugene Zeien]

The intent of the "brain_box" is to include only the region we are
certain will be within the brain.  This is not intended for measurements,
but rather to limit the region where the segmentation algorythm goes to
automatically identify chunks of gray matter, white matter, and csf.

The "cran_box" should be a better match for the whole brain.

Christoph Christmann wrote:
> Dear Ronald,
> 
> Thanks a lot for your suggestions!
> 
> We obtain only T1 and T2 data but at least this is mandatory for all of 
> our anatomic data. So we easily can include T2 data, too. I wasnt quite 
> sure if the data was used for the segmentation, too, even though I was 
> able to specify the T2 data in the segmentation dialog. I used the T2 
> data for the blood vessel definiton, too. I'll  go trough all steps in 
> the manual again and try the segmentation without prior skull stripping.
> 
> One question, however, remains: In the segmentation dialog there is a 
> specification of a standard box (talairach) which is too small for all 
> our brains (I couldnt figure out the reason for that - I append a 
> picture). Alternatively I used a mask (concurrent option) that I created 
> with a skull stripped image (by means of the image tools- threshold 
> option). Is there an alternative algorithm? What could be wrong with the 
> box?
> 
> Thanks again!
> 
> Sincerely
> 
> Christoph
> 
> 
> At Tuesday 24.01.2006 15:29, Ronald Pierson wrote:
> 
>> 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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