[ITK] Questions about ITK-Snap gaussian smoothing

[Dženan Zukić]

Hi Benedikt,

I trust VTK's docs more than a comment near the filter's invocation. But
you can easily test this by opening a highly anisotropic image (let's say Z
spacing 10x greater than X and Y spacing) with some e.g. sharp edges and
observing how the smoothing works.

Regards,
Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Tue, Jun 13, 2017 at 9:18 AM, Beyer, Benedikt Alexander <
benedikt.beyer at rwth-aachen.de> wrote:

> Hi Dženan and Paul,
>
>
>
> thank you for the Information about the mesh smoothing algorithm, that
> helped a lot. Unfortunately I don’t completely understand the source code,
> since I’m not a software developer.
>
>
>
> In the source code you linked it says that the maximum error parameter is
> ignored, so I assume that the value in the program settings has no effect
> on the smoothing.
>
> (https://sourceforge.net/p/itk-snap/src/ci/master/tree/
> Logic/Mesh/VTKMeshPipeline.cxx#l169)
>
>
>
> As for the sigma I still don’t entirely understand why the polygon model
> is not smoothed below a sigma of 0.67.
>
> In the preferences for ITK-SNAP at the 3D Rendering tab, there is a
> Gaussian image smoothing option. Activating this option will smooth the
> polygon model of a segmentation for sigma>=0.67.
>
>
>
> Also in the source code and documentation there seems to be contradicting
> information, because in vtkImageGaussianSmooth.h
> <https://gitlab.kitware.com/vtk/vtk/blob/master/Imaging/General/vtkImageGaussianSmooth.h>
> sigma is in pixel units and in VTKMeshPipeline.cxx#l166
> <https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.cxx#l166>
> it is in millimeters. Which information relates to the 3D Rendering option?
>
>
>
> Regards,
>
> Benedikt Beyer
>
>
>
> *Von:* Dženan Zukić [mailto:dzenanz at gmail.com]
> *Gesendet:* Dienstag, 30. Mai 2017 15:38
> *An:* Beyer, Benedikt Alexander <benedikt.beyer at rwth-aachen.de>
> *Cc:* community at itk.org; Paul Yushkevich <pyushkevich at gmail.com>
> *Betreff:* Re: [ITK] Questions about ITK-Snap gaussian smoothing
>
>
>
> Hi Benedikt,
>
>
>
> if you are asking about which mesh smoothing algorithm is used, I think
> this source code file answers that:
>
> https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/
> Mesh/VTKMeshPipeline.cxx#l167
>
>
>
> Its declaration
> <https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.h#l122>
> says it is an vtkImageGaussianSmooth
> <http://www.vtk.org/doc/nightly/html/classvtkImageGaussianSmooth.html>.
> If documentation is not enough, you can find its source code
> <https://gitlab.kitware.com/vtk/vtk/blob/master/Imaging/General/vtkImageGaussianSmooth.cxx>
> in VTK.
>
>
>
> As the sigma is passed into there as a parameter, I believe the
> user-modifiable preferences in the program control it.
>
>
>
> Paul (CC'd) might have more explanations.
>
>
>
> Regards,
>
> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
>
>
> On Tue, May 30, 2017 at 4:42 AM, Beyer, Benedikt Alexander <
> benedikt.beyer at rwth-aachen.de> wrote:
>
> Dear ITK community,
>
>
>
> I am currently writing an academic thesis at the RWTH Aachen University
> and I work with STL-data that is exported with ITK-Snap. A segmented
> structure is exported as an STL-file and then analyzed with VG Studio MAX.
> The data is used to determine measurement uncertainties created by gaussian
> filtering. To determine this uncertainty, I compare smoothed data to
> unsmoothed data.  I have a few questions regarding the gaussian image
> smoothing setting.
>
>
>
>    1. What gaussian filter algorithm does this option use? Eg. Recursive,
>    discrete, robust, etc.
>    2. Is this filter a linear or surface filter?
>    3. How big is the gaussian kernel? Eg. 3x3, 5x5, etc.
>    4. What does the “approximation error max” option do? It has no visual
>    effect on the segmentation.
>    5. There seems to be a threshold of the standard deviation at around
>    0.67. It seems that below this number no smoothing is applied. Is this
>    specific to the program, or is this dependend on the voxel size?
>    6. Are there any known influences on measurement uncertainty by
>    gaussian smoothing?
>
>
>
> Thank you in advance and with kind regards
>
> Benedikt Beyer
>
>
>
>
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