Hi Ping,
I was just wondering, if you want to do a VBM
analysis, you will definitely have to use non-linear
registration as FLIRT can not make all the structures
match across subjects. In other words, even if you put
all your images in a common space, you will not be
able to compare the data on a voxel-by-voxel basis.
You can have a look at the fsl-vbm manual, but I would
also recommend Ashburner et al., Voxel-based
morphometry- The methods (Neuroimage 2000) and Good et
al., A voxel-based morphometric study of ageing in 465
normal adult human brains (Neuroimage 2001) to better
understand the principles of VBM analysis.
Hope this helps,
Gwenaelle
> Dear every FSL expert:
>
> I have one patient group (some patient has white
> lesions in white matter). My final purpose is to
> normalize the patients to standard space, and could
> also have the white matter and gray matter of each
> patient in the standard space. Now I have following
> questions hope can get suggestions:
> 1) After the images were skull stripped (by
> Bet),which step should be the next, Flirt or Fast?
> Also the skull stripped results have holes sometime,
> is there any tool can improve the skull stripped
> results?
> 2) When I run Flirt, the default reference image is
> an MNI152_T1_2mm_brain image; if my input is T2
> image, should I select a T2 image as reference image
> or still use the default T1 reference image.
> Anyway, I cannot find any T2 reference image from
> fsl/data/standard/
>
> Thanks, any help is greatly appreciated!
> Ping
>
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