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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