White matter u segmentation

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White matter u segmentation

Tatjana Polgar
Dear "Slicer-ers"!
I have been trying to use the lesion segmentation module as described in the lupus lesion tutorial and it works fine for the tutorial dataset. Can someone tell what tutorial(s) do I need to use to get to the tutorial dataset on my own images, i.e. for brain extraction and binary correction to preprocess the images? 
I have tried several segmentation and filtering modules, also the edit box, however, none of them seem to do a good job on MS-related white matter lesions, kind of bread and butter neuroimaging.  
Your help is greatly appreciated.
Gabriella Szatmary, MD, PhD  

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Re: White matter u segmentation

madanrao
Hello Gabriella,

Have you tried Slicer3 EM segment tutorial ?

http://www.slicer.org/slicerWiki/images/2/2b/EMSegTutorial-AHM2008.ppt

Please check:

http://www.slicer.org/publications/item/view/1265

and download the brain atlas.

Hope this helps.

AM Mohan Rao

On Thu, Feb 17, 2011 at 5:37 AM, tanya <[hidden email]> wrote:
Dear "Slicer-ers"!
I have been trying to use the lesion segmentation module as described in the lupus lesion tutorial and it works fine for the tutorial dataset. Can someone tell what tutorial(s) do I need to use to get to the tutorial dataset on my own images, i.e. for brain extraction and binary correction to preprocess the images? 
I have tried several segmentation and filtering modules, also the edit box, however, none of them seem to do a good job on MS-related white matter lesions, kind of bread and butter neuroimaging.  
Your help is greatly appreciated.
Gabriella Szatmary, MD, PhD  

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Re: White matter u segmentation

inorton
In reply to this post by Tatjana Polgar
There was a question about this on slicer-users a few weeks ago. The short answer is that you have to work up your own preprocessing pipeline using a variety of tools. I don't think the answer made it to this list:

http://www.nitrc.org/forum/message.php?msg_id=3222

Note in particular that the models have only been trained on lupus data and thus may not be useful for other types of data without creation of a suitable training corpus.

In case you haven't seen these ms segmentation-related links:
http://www.ia.unc.edu/MSseg/

http://www.nitrc.org/projects/hammerwml
(and: http://slicer-users.65878.n3.nabble.com/White-Matter-Lesion-Segmentation-Module-for-MS-td979069.html )


On Wed, Feb 16, 2011 at 7:07 PM, tanya <[hidden email]> wrote:
Dear "Slicer-ers"!
I have been trying to use the lesion segmentation module as described in the lupus lesion tutorial and it works fine for the tutorial dataset. Can someone tell what tutorial(s) do I need to use to get to the tutorial dataset on my own images, i.e. for brain extraction and binary correction to preprocess the images? 
I have tried several segmentation and filtering modules, also the edit box, however, none of them seem to do a good job on MS-related white matter lesions, kind of bread and butter neuroimaging.  
Your help is greatly appreciated.
Gabriella Szatmary, MD, PhD  

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[hidden email]
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