Same here. 4 classes are not reliable for lesion segmentation.
As for multi-channel, it's not the more channels, the merrier. If you
have good GM/WM contrast in MPRAGE, stick with it for the optimal
segmentation results and use the -lm option in Sienax with manually
segmented lesion masks (registered to MPRAGE) from FLAIR or T2W image.
Gordon
On 1/5/11 4:34 PM, Keith Hulsey wrote:
> Hi Mark,
>
> Thanks for your response. I tried the multi-channel approach with 3 classes and with 4 classes. I didn't find it to be reliable either. I had wanted to check that I wasn't overlooking something obvious.
>
> Thanks again,
> Keith
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Wednesday, January 05, 2011 3:58 PM
> To: [log in to unmask]
> Subject: Re: [FSL] misclassification of white matter using FAST
>
> Hi Keith,
>
> If you have white matter intensity inhomogeneities that are disease- or
> age-related then FAST will not segment them properly, as you've found.
> The only solution we have is to manually identify the "lesions" by creating
> a manual mask (or any other way you know of) and then either excluding
> them from the FAST segmentation (setting them to zero is enough for this)
> or "filing" them with "normal" white matter intensities (ideally taken from the
> surrounding voxels) prior to segmentation.
>
> You could also try a multi-channel segmentation with 4 classes, but my
> experience is that it tends not to work very reliably.
>
> All the best,
> Mark
>
>
> On 5 Jan 2011, at 21:53, Keith Hulsey wrote:
>
>> I have used FAST to segment T1 weighted MPRAGE images into three classes. (Skull stripping and other image preparation has been done as used in SIENAX.) White matter regions which are very bright in FLAIR images tend to be darker in the T1 than other white matter. As a result FAST tends to misclassify this white matter as gray matter. Do you have any suggestions for automatically identifying FLAIR hyperintensities in the white matter that are misclassified as gray matter by FAST? I have MPRAGE, FLAIR and T2 images of my subjects.
>>
>> Thanks for your help,
>> Keith
>>
>
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>
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