Hello Ping,

i´ll present a poster at HBM 09, were I used FAST for segmenting white 
matter.
We´re working and optimizing the method right now.
Maybe we can discuss it there.
I´d be pleased to receive some feedback.


Regards

Oliver




p.s.: running slow didnt help me, so i needed to run fast!


WangPing schrieb:
> Dear Matt,
>
> Could you instruct me a little bit regarding the following scheme to 
> segment WM lesions from FLAIR using fast?
> I used command line: fast -n 3 myFLAIR.img , but the output images 
> seems try to get WM, GM, CSF.
> I do not how to use multi channels information, I do have T1, T2, PD, 
> FLAIR, the lesions seems only clear on FLAIR.
> Also, the option -t only applicable for (T1,T2, or PD), seems I cannot 
> elect FLAIR.
>
> Thanks, any help will be highly appreciated.
> Ping
> ------------------------------------------------------------------------
> Date: Tue, 16 Dec 2008 18:19:25 -0600
> From: [log in to unmask]
> Subject: Re: [FSL] white matter lesion segmentation on FLAIR image
> To: [log in to unmask]
>
> If you want to get only the lesions I would suggest just using the 
> FLAIR. You might need to play with the number of classes (default is 
> 3) to get the lesions as their own tissue class. This is the –n option 
> (e.g. –n 3 means to divide the image into three classes. It is 
> sufficient to type fast –n 3 FLAIRImageName.nii.gz to segment an 
> image. Also, you should brain extract the image first. Have a look at 
> the FAST manual page for more detailed instructions: 
> http://www.fmrib.ox.ac.uk/fsl/fast4/index.html
>
> Peace,
>
>
> Matt.
>
> ------------------------------------------------------------------------
>
> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On 
> Behalf Of *WangPing
> *Sent:* Tuesday, December 16, 2008 4:28 PM
> *To:* [log in to unmask]
> *Subject:* Re: [FSL] white matter lesion segmentation on FLAIR image
> *Importance:* High
>
> Thanks Matt, I would try. In the past I only know that FAST can 
> segment brain tissues into WM, GM, CSF. The lesion areas are more 
> clear on Flair modality, should I only use Flair, or need to combine 
> other modalities?
> BTW, what the type command line of FAST for this case (lesion 
> segmentation), thanks ahead for your help.
> Ping
>
> ------------------------------------------------------------------------
>
> Date: Tue, 16 Dec 2008 16:19:51 -0600
> From: [log in to unmask]
> Subject: Re: [FSL] white matter lesion segmentation on FLAIR image
> To: [log in to unmask]
>
> If they are of significantly different intensity from other tissues in 
> a particular modality, yes.
>
> Peace,
>
> Matt.
>
> ------------------------------------------------------------------------
>
> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On 
> Behalf Of *WangPing
> *Sent:* Tuesday, December 16, 2008 4:14 PM
> *To:* [log in to unmask]
> *Subject:* Re: [FSL] white matter lesion segmentation on FLAIR image
> *Importance:* High
>
> Matt, you mean FAST could segment the lesions? My Flair shows some 
> white matter lesions due to some diseases. Best, ping
>
> ------------------------------------------------------------------------
>
> Date: Tue, 16 Dec 2008 16:00:35 -0600
> From: [log in to unmask]
> Subject: Re: [FSL] white matter lesion segmentation on FLAIR image
> To: [log in to unmask]
>
> Have you tried using FAST (FMRIB's Automated Segmentation Tool)? It 
> will work with multiple image channels too.
>
> Peace,
>
> Matt.
>
> ------------------------------------------------------------------------
>
> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On 
> Behalf Of *WangPing
> *Sent:* Tuesday, December 16, 2008 3:33 PM
> *To:* [log in to unmask]
> *Subject:* [FSL] white matter lesion segmentation on FLAIR image
> *Importance:* High
>
> Dear FSL list,
>
> Sorry for bothering, I want to get help from the list regarding while 
> matter lesion segmentation on FLAIR image. Seems FSL has no this tool, 
> I am wondering if anyone could recommend one tool or give some 
> suggestions?
> P.S. Besides Flair, I do have T1, T2, PD, T2 for each subject.
>
> Best Regards.
> Ping Wang
>
> ------------------------------------------------------------------------
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-- 
Oliver Trebbe
Department of Neurology
University of Muenster
48129 Muenster, Germany