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FSL  September 2008

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Subject:

Re: Fslmaths -ero, how to change number of eroded voxels

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 23 Sep 2008 23:30:45 +0100

Content-Type:

text/plain

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text/plain (47 lines)

Hi Carlos,

Are you sure that you are getting more than one voxel eroded?
Are you running the erode on a binary mask?

It doesn't really make sense to use less than a 3x3x3 kernel (unless
you only wanted to erode in-plane).  So I don't think you probably
need to worry about the other kernel options.  The kernel is
centred on the voxel of interest, so that is why only odd values
are accepted.

You might want to combine an intensity thresholding operation with
your erosion (by generating separate masks and then combining
them in some way) if what you are doing is trying to tidy up portions
of a BET mask.

If this doesn't help, then please describe the situation in more detail.

All the best,
	Mark




On 23 Sep 2008, at 21:26, Carlos Faraco wrote:

> Mark,
>
> Actually thought about the 1x1x1 after I mentioned it and figured that
> wouldn't work either. Tried it and it didn't remove any voxels. So  
> how can I
> get it just remove 1 layer of 2x2x2 voxels? Or is the 3x3x3 already  
> doing
> that but just appears different?
>
> I would try it with the boxv, but it says to only use odd numbers.
>
> Could you give me a little bit more information on the kernel  
> funcion? For
> example, if the voxels are smaller than the specified kernel, but  
> not twice
> as small, will it jsut remove the first layer of voxels?
>
> Thanks,
>
> Carlos
>

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