Hi Ed,
The syntax for this bit of fslmaths is:
-kernel boxv <size>
so you just give it one number and it implements a box of
dimensions <size>x<size>x<size> in voxels.
It would not be able to interpret "3x3x1" correctly, and I'm not
sure what you would have got.
If you want 3x3x1 then use "-kernel 2D" as you've done before.
If you want some other, non-regular size (besides boxes, Gaussian
kernels or spheres) then you probably need to make your own
kernel image and use:
-kernel file <filename>
where filename points to an image of the kernel you want.
Hope this helps.
All the best,
Mark
On 9 Mar 2012, at 08:29, Ed wrote:
> Hi,
>
> I want to apply a median filter in 2D on a 3D volume with the following command:
>
> fslmath invol -kernel 2D -fmedian outvol
>
> That works fine. But now I want to use a different kernel size, instead of the default 3 x 3 x 1.
> So I first tried the following command to check the way a kernel can be specified:
>
> fslmath invol -kernel boxv 3x3x1 -fmedian outvol
>
> This should produce the same result as the first command but didn't. What is wrong?
>
> Regards
> Ed
>
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