smoothing segmentations

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smoothing segmentations

Murat Maga

Hi,

 

I have a general ‘best practice’ question. We are building models from manual segmentations of molar teeth from mice. These being manual segmentations, there are some ragged edges. The question is, should I do the smoothing at the label map stage and build the models without any smoothing. Or leave the label maps as it is do the smoothing at the model building stage?

 

I am inclined to do the second one, because there are six different labels, and smooth label map takes only one label at a time, which may create overlap issues. Leaving that aside, I would like to hear opinions.

 

These eventually be used for a statistical shape analysis, so we want to be as accurate as possible.

 

 

Best,

M


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Re: smoothing segmentations

Tamas Ungi-2

Hi,

 

My experience is that smoothing the surface model never gives as nice results as smoothing the image (label map) before generating surface.

But I don't have evidence to support this.

 

Tamas

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: November 17, 2015 6:16 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] smoothing segmentations

 

Hi,

 

I have a general ‘best practice’ question. We are building models from manual segmentations of molar teeth from mice. These being manual segmentations, there are some ragged edges. The question is, should I do the smoothing at the label map stage and build the models without any smoothing. Or leave the label maps as it is do the smoothing at the model building stage?

 

I am inclined to do the second one, because there are six different labels, and smooth label map takes only one label at a time, which may create overlap issues. Leaving that aside, I would like to hear opinions.

 

These eventually be used for a statistical shape analysis, so we want to be as accurate as possible.

 

 

Best,

M


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Re: smoothing segmentations

Aucoin, Nicole
In reply to this post by Murat Maga
Hi Murat,

The Model Maker module exposes an option to make sure that overlap doesn¹t
happen when smoothing models. In the Advanced tab, the Joint Smoothing
check box is useful in conjunction with the Generate All Models option. So
I¹d also vote for doing the smoothing at the model generation stage.

Nicole

So I¹d also vote for smoothing at the model generation stage.

On 11/17/15, 6:15 PM, "Murat Maga" <[hidden email]> wrote:

>Hi,
>
>I have a general Œbest practice¹ question. We are building models from
>manual segmentations of molar teeth from mice. These being manual
>segmentations, there
> are some ragged edges. The question is, should I do the smoothing at the
>label map stage and build the models without any smoothing. Or leave the
>label maps as it is do the smoothing at the model building stage?
>
>I am inclined to do the second one, because there are six different
>labels, and smooth label map takes only one label at a time, which may
>create overlap issues.
> Leaving that aside, I would like to hear opinions.
>
>These eventually be used for a statistical shape analysis, so we want to
>be as accurate as possible.
>
>
>Best,
>M
>

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