Re: [vmtk-users] 2 questions on segmentation

[Vikram M. <vv...@gm...>]

Thanks Luca, will look into your suggestions.

While waiting for your replies, I found another way outside of VMTK to
align my stl but the smoothing issue is still to be resolved.

Thanks again,
Vikram.



On Wed, May 1, 2013 at 1:13 PM, Luca Antiga <luc...@gm...> wrote:

> Hello Vikram,
>  thanks for your patience. Pretty busy couple of weeks.
>
> On Apr 23, 2013, at 2:51 PM, Vikram Mehta wrote:
>
> > Dear users,
> >
> > I have a couple of questions and I was hoping to get some advice on this.
> >
> > 1) Is there a way of aligning one of the ends of the reconstructed
> geometry with any of the axes?
> >     I use the geometries as a model for CFD simulations and some other
> processing methods in matlab. I need the vessel to be aligned with the x
> axis (for example) with the center of the inlet at the origin so that my
> boundary conditions are prescribed accurately.. I usually do it in other
> meshing softwares and I was wondering if this could be done in VMTK prior
> to exporting it as an STL file.
>
> There isn't a way to directly do this in vmtk using a script, but you can
> extract the origin and normal of a boundary using vmtkmeshboundaryinspector
> (you'll need to generate a mesh with vmtkmeshgenerator first, just use a
> fixed -edgelength - any mesh size will do if you just need to inspect the
> boundaries for the origin and normal), compute the transformation yourself
> and apply it with vmtkmeshtransform (by specifying the coefficients of the
> 4x4 transform matrix in lexicographic order with the -matrix option).
>
> > 2) Sometimes during the segmentation process, I end up with
> reconstructions with artificial bumps on them. Is there a way to
> INDIVIDUALLY smooth these bumps out ? Are there ways to avoid this ?  I do
> not want to over smooth the entire vessel and hence a way of smoothing just
> the rough/bumpy bits would be great !    Any suggestions would help !
>
> Yes, it happens sometimes, probably depending on the image features. A
> localized smoothing filter is something I thought about and wouldn't be
> hard to implement, but it isn't in vmtk right now.
> The way to get around this is to use vmtksurfaceclipper (preferably using
> -type sphere), clip a bump and then cap it using vmtksurfacecapper -method
> smooth.
>
> Best,
>
> Luca
>
> > Any help is greatly appreciated !
> >
> > Many thanks in advance
> > Vikram.
> >
> >
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