Re: [vmtk-users] 2 questions on segmentation

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

Hi Luca,

Thanks alot, that seemed to do the trick.

Cheers
Vikram.



On Mon, May 6, 2013 at 2:24 PM, Luca Antiga <luc...@or...> wrote:

> Hi Vikram,
>  I'm suggesting to pipe the vmtksurfacetriangle script right after
> vmtkmarchingcubes
>
> vmtkmarchingcubes -ifile some_file.vti --pipe vmtksurfacetriangle -ofile
> thesurface.vtp
>
> and see if this works.
>
> Luca
>
>
> On May 6, 2013, at 3:20 PM, Vikram Mehta wrote:
>
> Hi Luca,
>
> Yes these bumps/holes occured when I tried a smoothing script straight
> after marching cubes. It occurs at 3-4 spots on the reconstruction.
>
> Are you suggesting increasing the number of surface triangles ?
>
> Best
> Vikram.
>
>
>
> On Mon, May 6, 2013 at 2:13 PM, Luca Antiga <luc...@or...>wrote:
>
>> Hi Virkam,
>>  you haven't provided a lot of info on this, but this looks like a VTK
>> Marching Cubes issue that arises sometimes.
>> Try to use vmtksurfacetriangle right after vmtkmarchingcubes (and before
>> any other smoothing or other scripts).
>> Best,
>>
>> Luca
>>
>>
>> On May 6, 2013, at 3:09 PM, Vikram Mehta wrote:
>>
>> Thank you for your suggestions.
>>
>> I came across a new problem today - would you happen to know what causes
>> this ? And how I can repair my reconstruction ?
>>
>> Please find an image attached of the problem.
>>
>> Many thanks in advance
>> Vikram.
>>
>>
>>
>> On Thu, May 2, 2013 at 10:18 AM, Arjan Geers <aj...@gm...> wrote:
>>
>>> Hi Vikram,
>>>
>>> To smooth out bumps, you could also look into ReMESH (
>>> http://remesh.sourceforge.net/index.html). It allows you to select
>>> triangles of the surface mesh and smooth or remove only those. It also has
>>> a smooth hole filling algorithm.
>>>
>>> Arjan
>>>
>>>
>>> On Thu, May 2, 2013 at 11:00 AM, Vikram Mehta <vv...@gm...> wrote:
>>>
>>>> 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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>> <Screen Shot 2013-05-06 at 14.06.02.png>
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