Re: [vmtk-users] centerline extraction problem

[Luca Antiga <luca.antiga@or...>]

Hi Xiaoli,
 things got busy and this delayed my vmtk list time.

vmtkcenterlines works on any surface obtained in any way, only it needs to be orientable (i.e. you must be able to define outwards normals, unlike, say, a Klein bottle, https://en.wikipedia.org/wiki/Klein_bottle - this can also happen due to small-scale degeneracies) and manifold (i.e. each triangle edge must be share by at most two triangles).

In your case it was neither due to the segmentation artifacts inside the vessel.

So, yes, you can export an STL file from Amira, read it with vmtk and generate centerlines.


Luca


On Aug 21, 2013, at 6:39 PM, Xiaoli Zhang wrote:

> Hi Luca,
> 
> Thanks for pointing this out. Indeed this is the problem (at least it worked on the problematic dataset). It turned out there is some region inside the lumen not segmented, and that caused the problem. A quick question through: does vmtkcenterlines only work on surface created by vmtklevelsetsegmentation? Will it work on a manually segmented surface from Amira?
> 
> Just FYI, following are my steps for segmentation and centerline creation:
> 1. segment vessel wall from CT image (different from typical cast CT, only vessel wall has hyperintensity)
> 2. fill the lumen to include both vessel wall segmented above and its lumen
> 3. use vmtklevelsetsegmentation to generate deformable model from step 2's label field (not sure if it is necessary)
> 4. create centerline
> 
> Xiaoli
> 
> 
> 
> 
> On Fri, Aug 16, 2013 at 7:59 AM, Luca Antiga <luca.antiga@...> wrote:
> Hi Xiaoli,
>  I took a look at your surface. It's not immediately obvious, but there is a whole extra portion of surface inside of it (see screenshot taken with some translucency). This causes the algorithm to basically not work.
> I'm not sure how you got to this point, but I suggest you try to re-segment the surface making sure you obtain a single compact 3D model.
> Best,
> 
> Luca
> 
> <Screen Shot 2013-08-16 at 1.55.20 PM.png>
> 
> On Aug 16, 2013, at 3:55 AM, Xiaoli Zhang wrote:
> 
>> Hi Luca,
>> 
>> Attached is the surface file I am working on. The levelset segmentation wasn't working very well on the outer curvature of the arch, but that shouldn't be the problem. Even if I am only working on descending aorta, it still won't work.
>> 
>> Thanks,
>> Xiaoli
>> 
>> 
>> On Thu, Aug 15, 2013 at 5:09 PM, Luca Antiga <luca.antiga@...> wrote:
>> Hi, I see that there is a jagged line on the surface indicating that the surface is apparently not orientable, so normals flip where you see the dark line (since the shader interpolates normals). You can verify this in Paraview by applying the Glyph filter to the normals.
>> 
>> This would explain dificulties with the centerline algorithm, since normals are used when extracting the inner Delaunay diagram. 
>> 
>> Can you send the surface over? I can try to understand what's causing normals to flip.
>> 
>> Thanks
>> 
>> Luca
>> 
>> 
>> On 12/ago/2013, at 17:09, Xiaoli Zhang <zhangx29@...> wrote:
>> 
>>> Hi Luca,
>>> 
>>> Attached is the screenshots of the surface for centerline extraction from two different views. I have tried not to include aortic arch, but it didn't work either. Any suggestions will be appreciated.
>>> 
>>> Thanks,
>>> Xiaoli
>>> 
>>> On Sun, Aug 11, 2013 at 4:24 PM, Luca Antiga <luca.antiga@...> wrote:
>>> Hi Xiaoli, 
>>>  there must be a Voronoi diagram degeneracy somewhere. Feel free to post a screenshot of the model, I can try to point you to the candidate spots.
>>> Best,
>>> 
>>> Luca
>>> 
>>> 
>>> On Aug 8, 2013, at 7:50 PM, Xiaoli Zhang wrote:
>>> 
>>>> It seems someone has encountered the same problem before: http://www.mail-archive.com/vmtk-users@.../msg00283.html
>>>> 
>>>> I followed Luca's suggestions apply smoothing (tried passband of 0.01 and 0.1) and add a subdivision step before vmtkcenterlines. Still no luck, vmtkcenterlines script will never return. Any suggestions?
>>>> 
>>>> On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zhangx29@...> wrote:
>>>> I am new to vmtk and I am trying to extract centerline from CT image of the aorta. I prepared the surface in Amira and save as stl (ASCII) format. Then I ran vmtkcenterlines script and place a source point at inlet and a target point at outlet. vmtk then show "computing centerline" and staying for a very long time (>12 hours). The surface I am working on is a small file (stl size <1MB). 
>>>> 
>>>> Anyone can help please? I can send the screenshot of the surface and stl file if needed. Thanks.
>>>> 
>>>> Xiaoli
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Get 100% visibility into Java/.NET code with AppDynamics Lite!
>>>> It's a free troubleshooting tool designed for production.
>>>> Get down to code-level detail for bottlenecks, with <2% overhead. 
>>>> Download for free and get started troubleshooting in minutes. 
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk_______________________________________________
>>>> vmtk-users mailing list
>>>> vmtk-users@...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>> 
>>> 
>>> <C9N3_surface_centerline.jpg>
>>> ------------------------------------------------------------------------------
>>> Get 100% visibility into Java/.NET code with AppDynamics Lite!
>>> It's a free troubleshooting tool designed for production.
>>> Get down to code-level detail for bottlenecks, with <2% overhead. 
>>> Download for free and get started troubleshooting in minutes. 
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>> 
>> <C9N3.ls.mc.sm.vtp>
> 
> 

[vmtk-users] VTK 6

[Eduardo - Yahoo <camargo_rh@ya...>]

Hi!

Anybody knows if is possible integrate VTK 6.x with VMTK? And how could I
do that?

Thank you!

Atenciosamente,

Eduardo Camargo, M.Sc.

Analista de Sistemas
Instituto Nacional de Ciência e Tecnologia em
Medicina Assistida por Computação Científica
INCT-MACC  http://macc.lncc.br
Laboratório Nacional de Computação Científica
LNCC - http://www.lncc.br

[vmtk-users] get cross-sectional image perpendicular to centerline

[Xiaoli Zhang <zhangx29@gm...>]

Hi all,

I am wondering if there is a way in vmtk to get the cross-sectional image
(from 3D volumetric grayscale image: vti) following the centerline (.vtp)
and alway perpendicular to the centerline.

Thanks,
Xiaoli

Re: [vmtk-users] centerline extraction problem

[Xiaoli Zhang <zhangx29@gm...>]

Re: [vmtk-users] Obtaining parent vessel

[Luca Antiga <luca.antiga@or...>]

Hi Nikhil,
 you may want to check out this tutorial: http://www.vmtk.org/Tutorials/ParentVesselReconstruction
Best,

Luca

On Aug 20, 2013, at 5:05 PM, Nikhil Paliwal wrote:

> Hi,
> I have this diseased blood vessel with a small aneurysm on it (stl file). I want to get the original vessel without the aneurysm and then study the flow. Is there any function/group of functions in vmtk I can use to obtain the parent vessel.
> Thanks in advance.
> 
> Nikhil
> -- 
> Nikhil Paliwal
> PhD Candidate
> Department of Mechanical Engineering
> University at Buffalo
> ------------------------------------------------------------------------------
> Introducing Performance Central, a new site from SourceForge and 
> AppDynamics. Performance Central is your source for news, insights, 
> analysis and resources for efficient Application Performance Management. 
> Visit us today!
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Re: [vmtk-users] Obtaining parent vessel

[Nikhil Paliwal <npaliwal@bu...>]

Thanks a lot, exactly what I was looking for.
Nikhil


On Tue, Aug 20, 2013 at 11:09 AM, Luca Antiga <luca.antiga@...>wrote:

> Hi Nikhil,
>  you may want to check out this tutorial:
> http://www.vmtk.org/Tutorials/ParentVesselReconstruction
> Best,
>
> Luca
>
> On Aug 20, 2013, at 5:05 PM, Nikhil Paliwal wrote:
>
> > Hi,
> > I have this diseased blood vessel with a small aneurysm on it (stl
> file). I want to get the original vessel without the aneurysm and then
> study the flow. Is there any function/group of functions in vmtk I can use
> to obtain the parent vessel.
> > Thanks in advance.
> >
> > Nikhil
> > --
> > Nikhil Paliwal
> > PhD Candidate
> > Department of Mechanical Engineering
> > University at Buffalo
> >
> ------------------------------------------------------------------------------
> > Introducing Performance Central, a new site from SourceForge and
> > AppDynamics. Performance Central is your source for news, insights,
> > analysis and resources for efficient Application Performance Management.
> > Visit us today!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk_______________________________________________
> > vmtk-users mailing list
> > vmtk-users@...
> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>


-- 
Nikhil Paliwal
PhD Candidate
Department of Mechanical Engineering
University at Buffalo

[vmtk-users] Obtaining parent vessel

[Nikhil Paliwal <npaliwal@bu...>]

Hi,
I have this diseased blood vessel with a small aneurysm on it (stl file). I
want to get the original vessel without the aneurysm and then study the
flow. Is there any function/group of functions in vmtk I can use to obtain
the parent vessel.
Thanks in advance.

Nikhil
-- 
Nikhil Paliwal
PhD Candidate
Department of Mechanical Engineering
University at Buffalo

Re: [vmtk-users] Brain extraction in VMTK

[Luca Antiga <luca.antiga@or...>]

Hi Maria,
 skull stripping is out of vmtk's current scope.
You can find very effective skull stripping methods in 
- 3DSlicer (www.slicer.org, Foreground masking (BRAINS) module)
- BRAINSTools (https://github.com/BRAINSia/BRAINSTools)
- FreeSurfer (http://www.freesurfer.net/)
- SPM (http://www.fil.ion.ucl.ac.uk/spm/)

Hope this helps

Luca


On Aug 19, 2013, at 1:14 PM, Maria Grigorieva wrote:

> Hi all, I am working on brain MR, Ct and angiography image segmentation.
> My task is to extract brain segment, and remove the skull.
> How do I strip the skull in VMTK? Are there any modules for this?
> 
> Thank you!
> 
> 
> Maria Grigoryeva
> 
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite!
> It's a free troubleshooting tool designed for production.
> Get down to code-level detail for bottlenecks, with <2% overhead. 
> Download for free and get started troubleshooting in minutes. 
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[vmtk-users] Brain extraction in VMTK

[Maria Grigorieva <magsend@gm...>]

Hi all, I am working on brain MR, Ct and angiography image segmentation.
My task is to extract brain segment, and remove the skull.
How do I strip the skull in VMTK? Are there any modules for this?

Thank you!


Maria Grigoryeva

Re: [vmtk-users] centerline extraction problem

[Luca Antiga <luca.antiga@or...>]

Hi Xiaoli,
 I took a look at your surface. It's not immediately obvious, but there is a whole extra portion of surface inside of it (see screenshot taken with some translucency). This causes the algorithm to basically not work.
I'm not sure how you got to this point, but I suggest you try to re-segment the surface making sure you obtain a single compact 3D model.
Best,

Luca



On Aug 16, 2013, at 3:55 AM, Xiaoli Zhang wrote:

> Hi Luca,
> 
> Attached is the surface file I am working on. The levelset segmentation wasn't working very well on the outer curvature of the arch, but that shouldn't be the problem. Even if I am only working on descending aorta, it still won't work.
> 
> Thanks,
> Xiaoli
> 
> 
> On Thu, Aug 15, 2013 at 5:09 PM, Luca Antiga <luca.antiga@...> wrote:
> Hi, I see that there is a jagged line on the surface indicating that the surface is apparently not orientable, so normals flip where you see the dark line (since the shader interpolates normals). You can verify this in Paraview by applying the Glyph filter to the normals.
> 
> This would explain dificulties with the centerline algorithm, since normals are used when extracting the inner Delaunay diagram. 
> 
> Can you send the surface over? I can try to understand what's causing normals to flip.
> 
> Thanks
> 
> Luca
> 
> 
> On 12/ago/2013, at 17:09, Xiaoli Zhang <zhangx29@...> wrote:
> 
>> Hi Luca,
>> 
>> Attached is the screenshots of the surface for centerline extraction from two different views. I have tried not to include aortic arch, but it didn't work either. Any suggestions will be appreciated.
>> 
>> Thanks,
>> Xiaoli
>> 
>> On Sun, Aug 11, 2013 at 4:24 PM, Luca Antiga <luca.antiga@...> wrote:
>> Hi Xiaoli, 
>>  there must be a Voronoi diagram degeneracy somewhere. Feel free to post a screenshot of the model, I can try to point you to the candidate spots.
>> Best,
>> 
>> Luca
>> 
>> 
>> On Aug 8, 2013, at 7:50 PM, Xiaoli Zhang wrote:
>> 
>>> It seems someone has encountered the same problem before: http://www.mail-archive.com/vmtk-users@.../msg00283.html
>>> 
>>> I followed Luca's suggestions apply smoothing (tried passband of 0.01 and 0.1) and add a subdivision step before vmtkcenterlines. Still no luck, vmtkcenterlines script will never return. Any suggestions?
>>> 
>>> On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zhangx29@...> wrote:
>>> I am new to vmtk and I am trying to extract centerline from CT image of the aorta. I prepared the surface in Amira and save as stl (ASCII) format. Then I ran vmtkcenterlines script and place a source point at inlet and a target point at outlet. vmtk then show "computing centerline" and staying for a very long time (>12 hours). The surface I am working on is a small file (stl size <1MB). 
>>> 
>>> Anyone can help please? I can send the screenshot of the surface and stl file if needed. Thanks.
>>> 
>>> Xiaoli
>>> 
>>> ------------------------------------------------------------------------------
>>> Get 100% visibility into Java/.NET code with AppDynamics Lite!
>>> It's a free troubleshooting tool designed for production.
>>> Get down to code-level detail for bottlenecks, with <2% overhead. 
>>> Download for free and get started troubleshooting in minutes. 
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk_______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> 
>> 
>> <C9N3_surface_centerline.jpg>
>> ------------------------------------------------------------------------------
>> Get 100% visibility into Java/.NET code with AppDynamics Lite!
>> It's a free troubleshooting tool designed for production.
>> Get down to code-level detail for bottlenecks, with <2% overhead. 
>> Download for free and get started troubleshooting in minutes. 
>> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
>> _______________________________________________
>> vmtk-users mailing list
>> vmtk-users@...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> <C9N3.ls.mc.sm.vtp>

Re: [vmtk-users] bifurcation plane

[Luca Antiga <luca.antiga@or...>]

Hi Laura,
 yes, the numbering you laid out is correct.

Curvature is indeed the inverse of the radius of curvature of the osculating circle at each point on the curve. Of course once you average over an entire tract and then average the tracts of a branch that interpretation loses its locality, although it might still be useful for visualizing things in your head.

BTW, remember to compute curvature by activating smoothing (-smoothing 1), in order to suppress noise while taking derivatives.

Best,

Luca


On 12/ago/2013, at 19:40, Laura Ellwein <laura.ellwein@...> wrote:

> nHi Luca,
> 
> This does help, I think I also had to go back and reread what exactly a "tract" is. So it looks like what I want is the vmtkbranchgeometry output to get curvature for that branch. It appears that for my coronary bifurcations, the groupId for the parent vessel is 0, the daughter is 2, and the side branch is 3. Then the birfurcation group is probably 1, correct?
> And it is the inverse of "radius of curvature", correct?
> 
> Thanks for your help.
> 
> 
> - Laura
> 
> 
> On Sun, Aug 11, 2013 at 4:22 PM, Luca Antiga <luca.antiga@...> wrote:
>> Hello Laura,
>>  what happens in vmtkbranchgeometry regarding curvature is the following:
>> - the curvature of each centerline tract is computed (as a continuous quantity along the line segment - same as for vmtkcenterlinegeometry)
>> - the curvature of each tract is averaged over the tract
>> - the average curvature for all tracts belonging to the same group id is averaged to produce the branch curvature value you read in output
>> I hope this clarifies things, feel free to ask for more details.
>> Best regards
>> 
>> Luca
>> 
>> 
>> On Aug 8, 2013, at 6:05 PM, Laura Ellwein wrote:
>> 
>>> Hi Luca,
>>> 
>>> I have a question about the curvature calculation that was brought up by another user a few months ago, so I am appending his email.
>>> 
>>> I understand that using 'vmtkcenterlinegeometry' gives a curvature value calculated for each centerline point, and I believe 'vmtkbranchgeometry' gives an average for each branch. I am looking for the latter for a population of coronary bifurcations and I want to make sure I am using the scripts correctly. In theory, should the curvature values using 'vmtkcenterlinegeometry' average to equal those output with 'vmtkbranchgeometry' assuming I split the branches in the right place? I can very clearly parse out the 'side branch' because of the break in the XYZ coordinates so I compared the average curvature output from the branch script and what I computed from the centerline script... they were not at all the same. Can you clarify these scripts a bit more and/or point me to a reference if that is easier?
>>> 
>>> Thank you,
>>> Laura Ellwein
>>> VCU
>>> 
>>> 
>>> - Laura
>>> 
>>> 
>>> On Wed, May 8, 2013 at 4:37 AM, qiang zeng <zengqiang2006@...> wrote:
>>>> 
>>>> Dear Luca,
>>>> Yeah, you are right when i am checking for what you said.
>>>> thank you.
>>>> YiQiang
>>>> 
>>>> --- 13年5月8日，周三, Luca Antiga <luca.antiga@...> 写道：
>>>> 
>>>> 发件人: Luca Antiga <luca.antiga@...>
>>>> 主题: Re: [vmtk-users] bifurcation plane
>>>> 收件人: "qiang zeng" <zengqiang2006@...>
>>>> 抄送: vmtk-users@...
>>>> 日期: 2013年5月8日,周三,下午4:02
>>>> 
>>>> 
>>>> Hi YiQiang,
>>>>  I don't think this is what happens: you only get one value per GroupId with the vmtkbranchgeometry script,
>>>> while with vmtkcenterlinegeometry you get a curvature value for each point on each centerline.
>>>> vmtkbranchgeometry looks at all centerlines tracts in a group and averages their curvature value.
>>>> 
>>>> Luca
>>>> 
>>>> 
>>>> On May 8, 2013, at 4:48 AM, qiang zeng wrote:
>>>> 
>>>>> 
>>>>> bifurcation plane is work well.
>>>>>  
>>>>> another problem, when I caculate the curvature using the following script "vmtkcenterlinegeometry -ifile foo_cl.vtp -smoothing 1 -ofile foo_clgm.vtp", I just get the one curvature value for every GroupIds. but in generally, the curve for every GroupIds has different points (point1, point2,...) and every point in curve has a curvature value respectively.
>>>>> So how to understand this approach considering one curvature value as curvature value of entire GroupIds?
>>>>>  
>>>>> YiQiang  
>>>>> --- 13年5月7日，周二, Luca Antiga <luca.antiga@...> 写道：
>>>>> 
>>>>> 发件人: Luca Antiga <luca.antiga@...>
>>>>> 主题: Re: [vmtk-users] bifurcation plane
>>>>> 收件人: "qiang zeng" <zengqiang2006@...>
>>>>> 抄送: vmtk-users@...
>>>>> 日期: 2013年5月7日,周二,下午2:40
>>>>> 
>>>>> Hi YiQiang,
>>>>>  point1 and point2 are any two points on the plane away from the origin.
>>>>> You could do
>>>>> point1 = origin + upnormal
>>>>> point2 = origin + normal x upnormal
>>>>> where x indicates the cross product.
>>>>> 
>>>>> Luca
>>>>> 
>>>>> On 07/mag/2013, at 07:39, qiang zeng <zengqiang2006@...> wrote:
>>>>> 
>>>>>> 
>>>>>> Usig the command line:
>>>>>>  
>>>>>> vmtkbranchextractor -ifile foo_cl.vtp -radiusarray@ MaximumInscribedSphereRadius --pipe
>>>>>> vmtkbifurcationreferencesystems -ofile foo_rs.dat
>>>>>>  
>>>>>> I get the one point and two vectors, then I fill the coordinate into the Paraview (point -> Origin, Normal -> Point1 and Upnormal -> Point2) ?
>>>>>> Best
>>>>>> YiQiang
>>>>>> 
>>>>>> --- 13年5月6日，周一, Luca Antiga <luca.antiga@...> 写道：
>>>>>> 
>>>>>> 发件人: Luca Antiga <luca.antiga@...>
>>>>>> 主题: Re: [vmtk-users] bifurcation plane
>>>>>> 收件人: "qiang zeng" <zengqiang2006@...>
>>>>>> 抄送: vmtk-users@...
>>>>>> 日期: 2013年5月6日,周一,下午8:54
>>>>>> 
>>>>>> Hi YiQiang,
>>>>>>  the figure you attached was created in Paraview using the origin and normal of the plane
>>>>>> as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
>>>>>> in Paraview (Sources->Plane). It works well if the number of figures you create is small.
>>>>>> 
>>>>>> If you need to create the visualization automatically you'll need to write VTK code and use the
>>>>>> vtkPlaneSource class to create the plane.
>>>>>> The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
>>>>>> Examples: 
>>>>>> http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
>>>>>> http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource
>>>>>> 
>>>>>> Best,
>>>>>> 
>>>>>> Luca
>>>>>> 
>>>>>> 
>>>>>> On May 6, 2013, at 9:40 AM, qiang zeng wrote:
>>>>>> 
>>>>>>> 
>>>>>>> Hi all,
>>>>>>> When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
>>>>>>> Does anyone know a way to do this?
>>>>>>> Best,
>>>>>>> YiQiang
>>>>>>> <bifurcation plane.jpg>------------------------------------------------------------------------------
>>>>>>> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
>>>>>>> Get 100% visibility into your production application - at no cost.
>>>>>>> Code-level diagnostics for performance bottlenecks with <2% overhead
>>>>>>> Download for free and get started troubleshooting in minutes.
>>>>>>> http://p.sf.net/sfu/appdyn_d2d_ap1_______________________________________________
>>>>>>> vmtk-users mailing list
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>>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 

Re: [vmtk-users] centerline extraction problem

[Luca Antiga <luca.antiga@gm...>]

Hi, I see that there is a jagged line on the surface indicating that the surface is apparently not orientable, so normals flip where you see the dark line (since the shader interpolates normals). You can verify this in Paraview by applying the Glyph filter to the normals.

This would explain dificulties with the centerline algorithm, since normals are used when extracting the inner Delaunay diagram. 

Can you send the surface over? I can try to understand what's causing normals to flip.

Thanks

Luca


On 12/ago/2013, at 17:09, Xiaoli Zhang <zhangx29@...> wrote:

> Hi Luca,
> 
> Attached is the screenshots of the surface for centerline extraction from two different views. I have tried not to include aortic arch, but it didn't work either. Any suggestions will be appreciated.
> 
> Thanks,
> Xiaoli
> 
> On Sun, Aug 11, 2013 at 4:24 PM, Luca Antiga <luca.antiga@...> wrote:
>> Hi Xiaoli, 
>>  there must be a Voronoi diagram degeneracy somewhere. Feel free to post a screenshot of the model, I can try to point you to the candidate spots.
>> Best,
>> 
>> Luca
>> 
>> 
>> On Aug 8, 2013, at 7:50 PM, Xiaoli Zhang wrote:
>> 
>>> It seems someone has encountered the same problem before: http://www.mail-archive.com/vmtk-users@.../msg00283.html
>>> 
>>> I followed Luca's suggestions apply smoothing (tried passband of 0.01 and 0.1) and add a subdivision step before vmtkcenterlines. Still no luck, vmtkcenterlines script will never return. Any suggestions?
>>> 
>>> On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zhangx29@...> wrote:
>>>> I am new to vmtk and I am trying to extract centerline from CT image of the aorta. I prepared the surface in Amira and save as stl (ASCII) format. Then I ran vmtkcenterlines script and place a source point at inlet and a target point at outlet. vmtk then show "computing centerline" and staying for a very long time (>12 hours). The surface I am working on is a small file (stl size <1MB). 
>>>> 
>>>> Anyone can help please? I can send the screenshot of the surface and stl file if needed. Thanks.
>>>> 
>>>> Xiaoli
>>> 
>>> ------------------------------------------------------------------------------
>>> Get 100% visibility into Java/.NET code with AppDynamics Lite!
>>> It's a free troubleshooting tool designed for production.
>>> Get down to code-level detail for bottlenecks, with <2% overhead. 
>>> Download for free and get started troubleshooting in minutes. 
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk_______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> <C9N3_surface_centerline.jpg>
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite!
> It's a free troubleshooting tool designed for production.
> Get down to code-level detail for bottlenecks, with <2% overhead. 
> Download for free and get started troubleshooting in minutes. 
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
> _______________________________________________
> vmtk-users mailing list
> vmtk-users@...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] RAS transformation

[Hoppe, Anna L <anna-hoppe@ui...>]

Re: [vmtk-users] centerline extraction problem

[Xiaoli Zhang <zhangx29@gm...>]

Re: [vmtk-users] Elliptical cross-sections

[Luca Antiga <luca.antiga@or...>]

Hi Oliver,
 there's something you can do to characterize elliptical cross-sections.
First compute centerlines, then use 
vmtkcenterlinesections -ifile model.vtp -centerlinesfile centerlines.vtp -ofile sections.vtp
The sections dataset will contain min size and max size (taken as the min and max distance
of the section to the intersection of the centerline and the section plane) and area.
Hope this helps,

Luca

On Aug 10, 2013, at 5:06 AM, Oliver Maclaren wrote:

> Hi,
> I'm sure this question has probably come up a few times but I haven't been able to find an answer. I am hoping someone could point me in the right direction.
> 
> I have worked through most of the tutorials and managed to reconstruct my object of interest - a lumen structure with multiple interconnected tubular parts - as well as extract the maximum inscribed sphere radius along each branch. 
> 
> However the cross section along each 'tube' is in fact quite elliptical and I was hoping to have a measure of the the larger dimension along each tube. What is the easiest way to do this? Sorry if the question has been addressed somewhere obvious but most that I have seen emphasizes the maximum inscribed radius and circular cross-sections.
> 
> Thanks,
> Oliver
> 
> -- 
> Oliver Maclaren BE(Hons)
> PhD Candidate
> Auckland Bioengineering Institute
> The University of Auckland
> New Zealand
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Re: [vmtk-users] (no subject)

[Luca Antiga <luca.antiga@or...>]

Hi Evan,
 it's quite extensive, but I'd give it a try. If it doesn't work, this looks like the right job for a thinning algorithm in image space (not yet in vmtk, although it could be a nice addition), I can point you to some ITK classes that implement it, if you're interested.
Let us know how things go with this dataset.
Thanks,

Luca

On Aug 9, 2013, at 7:47 PM, Evan Kao wrote:

> Hello VMTK-users,
> 
> A colleague has asked about skeletonizing a dense microvascular network (see image).  Is it sensible to use VMTK (like vmtknetworkextraction?) for something this extensive?
> 
> <microvasc.png>
> 
> Thanks,
> Evan Kao
> ------------------------------------------------------------------------------
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Re: [vmtk-users] centerline extraction problem

[Luca Antiga <luca.antiga@or...>]

Hi Xiaoli, 
 there must be a Voronoi diagram degeneracy somewhere. Feel free to post a screenshot of the model, I can try to point you to the candidate spots.
Best,

Luca


On Aug 8, 2013, at 7:50 PM, Xiaoli Zhang wrote:

> It seems someone has encountered the same problem before: http://www.mail-archive.com/vmtk-users@.../msg00283.html
> 
> I followed Luca's suggestions apply smoothing (tried passband of 0.01 and 0.1) and add a subdivision step before vmtkcenterlines. Still no luck, vmtkcenterlines script will never return. Any suggestions?
> 
> On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zhangx29@...> wrote:
> I am new to vmtk and I am trying to extract centerline from CT image of the aorta. I prepared the surface in Amira and save as stl (ASCII) format. Then I ran vmtkcenterlines script and place a source point at inlet and a target point at outlet. vmtk then show "computing centerline" and staying for a very long time (>12 hours). The surface I am working on is a small file (stl size <1MB). 
> 
> Anyone can help please? I can send the screenshot of the surface and stl file if needed. Thanks.
> 
> Xiaoli
> 
> ------------------------------------------------------------------------------
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Re: [vmtk-users] bifurcation plane

[Luca Antiga <luca.antiga@or...>]

Hello Laura,
 what happens in vmtkbranchgeometry regarding curvature is the following:
- the curvature of each centerline tract is computed (as a continuous quantity along the line segment - same as for vmtkcenterlinegeometry)
- the curvature of each tract is averaged over the tract
- the average curvature for all tracts belonging to the same group id is averaged to produce the branch curvature value you read in output
I hope this clarifies things, feel free to ask for more details.
Best regards

Luca


On Aug 8, 2013, at 6:05 PM, Laura Ellwein wrote:

> Hi Luca,
> 
> I have a question about the curvature calculation that was brought up by another user a few months ago, so I am appending his email.
> 
> I understand that using 'vmtkcenterlinegeometry' gives a curvature value calculated for each centerline point, and I believe 'vmtkbranchgeometry' gives an average for each branch. I am looking for the latter for a population of coronary bifurcations and I want to make sure I am using the scripts correctly. In theory, should the curvature values using 'vmtkcenterlinegeometry' average to equal those output with 'vmtkbranchgeometry' assuming I split the branches in the right place? I can very clearly parse out the 'side branch' because of the break in the XYZ coordinates so I compared the average curvature output from the branch script and what I computed from the centerline script... they were not at all the same. Can you clarify these scripts a bit more and/or point me to a reference if that is easier?
> 
> Thank you,
> Laura Ellwein
> VCU
> 
> 
> - Laura
> 
> 
> On Wed, May 8, 2013 at 4:37 AM, qiang zeng <zengqiang2006@...> wrote:
> Dear Luca,
> Yeah, you are right when i am checking for what you said.
> thank you.
> YiQiang
> 
> --- 13年5月8日，周三, Luca Antiga <luca.antiga@...> 写道：
> 
> 发件人: Luca Antiga <luca.antiga@...>
> 主题: Re: [vmtk-users] bifurcation plane
> 收件人: "qiang zeng" <zengqiang2006@...>
> 抄送: vmtk-users@...
> 日期: 2013年5月8日,周三,下午4:02
> 
> 
> Hi YiQiang,
>  I don't think this is what happens: you only get one value per GroupId with the vmtkbranchgeometry script,
> while with vmtkcenterlinegeometry you get a curvature value for each point on each centerline.
> vmtkbranchgeometry looks at all centerlines tracts in a group and averages their curvature value.
> 
> Luca
> 
> 
> On May 8, 2013, at 4:48 AM, qiang zeng wrote:
> 
>> bifurcation plane is work well.
>>  
>> another problem, when I caculate the curvature using the following script "vmtkcenterlinegeometry -ifile foo_cl.vtp -smoothing 1 -ofile foo_clgm.vtp", I just get the one curvature value for every GroupIds. but in generally, the curve for every GroupIds has different points (point1, point2,...) and every point in curve has a curvature value respectively.
>> So how to understand this approach considering one curvature value as curvature value of entire GroupIds?
>>  
>> YiQiang  
>> --- 13年5月7日，周二, Luca Antiga <luca.antiga@...> 写道：
>> 
>> 发件人: Luca Antiga <luca.antiga@...>
>> 主题: Re: [vmtk-users] bifurcation plane
>> 收件人: "qiang zeng" <zengqiang2006@...>
>> 抄送: vmtk-users@...
>> 日期: 2013年5月7日,周二,下午2:40
>> 
>> Hi YiQiang,
>>  point1 and point2 are any two points on the plane away from the origin.
>> You could do
>> point1 = origin + upnormal
>> point2 = origin + normal x upnormal
>> where x indicates the cross product.
>> 
>> Luca
>> 
>> On 07/mag/2013, at 07:39, qiang zeng <zengqiang2006@...> wrote:
>> 
>>> Usig the command line:
>>>  
>>> vmtkbranchextractor -ifile foo_cl.vtp -radiusarray@ MaximumInscribedSphereRadius --pipe
>>> vmtkbifurcationreferencesystems -ofile foo_rs.dat
>>>  
>>> I get the one point and two vectors, then I fill the coordinate into the Paraview (point -> Origin, Normal -> Point1 and Upnormal -> Point2) ?
>>> Best
>>> YiQiang
>>> 
>>> --- 13年5月6日，周一, Luca Antiga <luca.antiga@...> 写道：
>>> 
>>> 发件人: Luca Antiga <luca.antiga@...>
>>> 主题: Re: [vmtk-users] bifurcation plane
>>> 收件人: "qiang zeng" <zengqiang2006@...>
>>> 抄送: vmtk-users@...
>>> 日期: 2013年5月6日,周一,下午8:54
>>> 
>>> Hi YiQiang,
>>>  the figure you attached was created in Paraview using the origin and normal of the plane
>>> as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
>>> in Paraview (Sources->Plane). It works well if the number of figures you create is small.
>>> 
>>> If you need to create the visualization automatically you'll need to write VTK code and use the
>>> vtkPlaneSource class to create the plane.
>>> The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
>>> Examples: 
>>> http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
>>> http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource
>>> 
>>> Best,
>>> 
>>> Luca
>>> 
>>> 
>>> On May 6, 2013, at 9:40 AM, qiang zeng wrote:
>>> 
>>>> Hi all,
>>>> When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
>>>> Does anyone know a way to do this?
>>>> Best,
>>>> YiQiang
>>>> <bifurcation plane.jpg>------------------------------------------------------------------------------
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>>>> Get 100% visibility into your production application - at no cost.
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>>> 
> 
> 

[vmtk-users] Elliptical cross-sections

[Oliver Maclaren <omac010@au...>]

Hi,
I'm sure this question has probably come up a few times but I haven't been
able to find an answer. I am hoping someone could point me in the right
direction.

I have worked through most of the tutorials and managed to reconstruct my
object of interest - a lumen structure with multiple interconnected
tubular parts - as well as extract the maximum inscribed sphere radius
along each branch.

However the cross section along each 'tube' is in fact quite elliptical and
I was hoping to have a measure of the the larger dimension along each tube.
What is the easiest way to do this? Sorry if the question has been
addressed somewhere obvious but most that I have seen emphasizes the
maximum inscribed radius and circular cross-sections.

Thanks,
Oliver

-- 
Oliver Maclaren BE(Hons)
PhD Candidate
Auckland Bioengineering Institute
The University of Auckland
New Zealand

[vmtk-users] (no subject)

[Evan Kao <tossin@gm...>]

Re: [vmtk-users] centerline extraction problem

[Xiaoli Zhang <zhangx29@gm...>]

It seems someone has encountered the same problem before:
http://www.mail-archive.com/vmtk-users@.../msg00283.html

I followed Luca's suggestions apply smoothing (tried passband of 0.01 and
0.1) and add a subdivision step before vmtkcenterlines. Still no luck,
vmtkcenterlines script will never return. Any suggestions?

On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zhangx29@...> wrote:

> I am new to vmtk and I am trying to extract centerline from CT image of
> the aorta. I prepared the surface in Amira and save as stl (ASCII) format.
> Then I ran vmtkcenterlines script and place a source point at inlet and a
> target point at outlet. vmtk then show "computing centerline" and staying
> for a very long time (>12 hours). The surface I am working on is a small
> file (stl size <1MB).
>
> Anyone can help please? I can send the screenshot of the surface and stl
> file if needed. Thanks.
>
> Xiaoli
>

Re: [vmtk-users] centerline extraction problem

[Xiaoli Zhang <zhangx29@gm...>]

Some more information about the problem: vmtkcenterlines sometimes throw
out following warning during the process.

Generic Warning: In /projects/mice/xzhang/VTK/src/Common/vtkMath.cxx, Line
544
Unable to factor linear system

Warning: In /projects/mice/xzhang/VTK/src/VTK/Graphics/vtkDelaunay3D.cxx,
Line 487
vtkDelaunay3D (0x59af7e0): 1 degenerate triangles encountered, mesh quality
suspect

Appreciate if anyone can suggest some solutions. Thanks.

On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zhangx29@...> wrote:

> I am new to vmtk and I am trying to extract centerline from CT image of
> the aorta. I prepared the surface in Amira and save as stl (ASCII) format.
> Then I ran vmtkcenterlines script and place a source point at inlet and a
> target point at outlet. vmtk then show "computing centerline" and staying
> for a very long time (>12 hours). The surface I am working on is a small
> file (stl size <1MB).
>
> Anyone can help please? I can send the screenshot of the surface and stl
> file if needed. Thanks.
>
> Xiaoli
>

Re: [vmtk-users] RAS transformation

[Luca Antiga <luca.antiga@or...>]

Hello Anna,
 sorry for the wait.

On Aug 2, 2013, at 9:08 PM, Hoppe, Anna L wrote:

> Hi Luca (again), 
> 
> I have another update for you:
> 
> 1. Using the script: 
> vmtkimagereader -ifile /path/image_001.dcm --pipe vmtkimagewriter /path/image001.mha for some reason results in a .mha that is misaligned from the original image_001 volume. 

You mean from the volume that was read using -f dicom, right?

> So this means that using the following 2 scripts: 
> vmtkimagereader -ifile /path/image_001.dcm --pipe vmtklevelsetsegmentation --pipe vmtkmarchingcubes -i @.o -ofile /path/test_unaligned.vtp
> 
> followed by:
> vmtkimagereader -ifile /path/image_001.dcm --pipe vmtksurfacetransformtoras -ifile /path/test_unaligned.vtp -ofile /path/test_aligned.vtp
> 
> Actually does result in a surface which is aligned with image_001 volume.

Good, this is how it is supposed to work.

> In other words, if the syntax vmtkimagereader -ifile is used for both the segmentation/reconstruction and the transformation back to RAS then everything works as it should and the transformed surface aligns with the image volume from whence it came (in RAS space of course).  Sorry, I know this is what you telling me the other day, I was just comparing against the wrong thing yesterday.

No worries!

> The light at the end of the tunnel is this: if I re-do my segmentations after first reading in the image using vmtkimageviewer -ifile then I'll be able to transform the surface back to RAS like I want. 
> 
> 2.At this point I still don't know how to get the models reconstructed via the vmtkimagereader -f dicom -d syntax back to RAS, or the .vti segmentation files for that matter. What I was thinking was that if the RAS transform matrix for these models simply involved a translation by the origin in xyz space, I could just manually manipulate the transformation matrix until I found an exact match. I've tried to manually manipulate this matrix using the following script: 
> 
> vmtkimagereader -ifile  /path/image_001.dcm --pipe vmtksurfacetransformtoras -ifile /path/model_from_vmtkimagereader_dicom_syntax.vtp -matrix 1.0 -2.0510340648094427e-10 0.0 -90.625 2.0510340648094427e-10 1.0 0.0 -62.9 0.0 0.0 1.0 -55.541767 0.0 0.0 0.0 1.0 -ofile /path/model_transformedtoras.vtp
> 
> then manually change the -matrix. What I've found from reading online is that the matrix is a 4X4 matrix where the fourth value in every row corresponds to the an x,y,z translation. So I cut/copied the XyzToRasMatrixCoefficients that were the output from vmtkimagereader, then pasted them after -matrix. I proceeded to manipulate the fourth matrix value in every row to be either the respective origin coordinate or a multiple.  I then loaded the image volume dicoms into Slicer, made a quickie model, then loaded in model_transformedtoras.vtp to see how the 2 compared. What I found is that the transformation matrix seems to incorporate the x and z origin values, but not the y. In fact to make the 2 models align by eye-balling I used a seemingly arbitrarynumber in its place.
> 
> My question is: do you know anyway to do this? Or is this why you started off by saying there's really no way to back calculate this transformation matrix the other day...

What you write about the y value is weird, it shouldn't work this way.

Question: when you load up the two volumes (the -ifile one and the -f dicom one) using vmtkimageviewer, do you see any of the axes flipped? (by flipped I mean, like liver on the left vs on the right - I know you're processing brain images, just using the liver for clarity).

Also, if you look at the i,j,k cursor coordinates while you're clicking on the image, does the first, second and third coordinate correspond in terms of spatial directions between the two images?

I'm asking because if the answer is yes, then you should be able to just align by translation. Otherwise you'll have to flip axes and things could get a bit trickier.

Feel free to send the two sample images over.

Best,

Luca


> Also, you can feel free to disregard my previous email - I wouldn't want you to read 2 very long emails :-) 

The questions above should also help for the other message :-)


> Anna
> From: Hoppe, Anna L [anna-hoppe@...]
> Sent: Thursday, August 01, 2013 4:47 PM
> To: vmtk-users@...
> Cc: Johnson, Kevin R
> Subject: [vmtk-users] RAS transformation
> 
> Hi Luca,
> 
> I worked on the xyz to RAS transformation problem. Here are two updates:
> 
> 1: I used the 2 different syntax's of vmtkimagereader (vmtkimagereader -ifile /path/image_001.dcm --pipe vmtkimagewriter /path/image001.mha and vmtkimagereader -f dicom -d /path/ --pipe vmtkimagewriter /path/image002.mha). I was able to use vmtkimagereader -f dicom -d /path/ -flip 1 1 0 --pipe vmtkimagewriter /path/image002.mha to orient the image volume correctly relative to the image volume read in using the -ifile syntax.
> 
> Here's a photo of the two image volumes in 3D Slicer (note that I just made an isosurface model of each in slicer and that's what you're looking at. Green is the isosurface corresponding to the image volume read in via -ifile and purple is the isosurface of the volume read in by -f dicom -d)
> <ifile_model_dicom_model2.jpeg>
> >From the photo you can see that the two are still displaced, but my suspicion is that the offset is just by the origin coordinates (90.625, 137.167068, -55.541767, or some multiple of these). Yet when I try and use vmtkimagereader -f dicom -d /path/ -origin 90.625000 137.167068 -55.541767 the image volume is still in the same location it was without using the -origin flag. Does -origin not work when -f dicom -d is used?  Is there a way to even align these two image volumes with the flags in vmtkimagereader? 
> 
> 
> 
> 2. Just to see if reading in an image volume using vmtkimagereader -ifile /path/image_001.dcm, making a model using vmtklevelsetsegmenation and vmtkmarchingcubes, and then using vmtksurfacetransformtoras to transform from xyz to RAS results in an aligned model & image in RAS space, I tried the following 2 scripts:
> 
> vmtkimagereader -ifile /path/image_001.dcm --pipe vmtklevelsetsegmentation --pipe vmtkmarchingcubes -i @.o -ofile /path/test_unaligned.vtp
> 
> followed by:
> vmtkimagereader -ifile /path/image_001.dcm --pipe vmtksurfacetransformtoras -ifile /path/test_unaligned.vtp -ofile /path/test_aligned.vtp
> 
> The vmtksurfacetransformtoras output (test_aligned.vtp) is shown in gray in the following image (recall that the green model is the isosurface corresponding to vmtkimagereader -ifile /path/image001.dcm --pipe vmtkimagewriter /path/image001.mha):
> <ifile_model_dicom_model3.jpeg>
> So even reading an image volume via -ifile, making a model via vmtk, and then running vmtksurfacetransformtoras results in misalignment -seems like this should not have happened, am I missing something here?
> 
> Thanks for everything - it is appreciated!
> Anna
> 
> 
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Re: [vmtk-users] Maximum inscribed sphere radius

[Luca Antiga <luca.antiga@or...>]

Hi Nikhil,
 look at this tutorial:
http://www.vmtk.org/Tutorials/Centerlines/
for generating centerlines from a surface. Centerlines are the envelope of maximum inscribed spheres and carry the radius of the sphere at each point.
To extract the largest radius, just output the centerlines file with a .dat extension, which will essentially produce a CSV file with the radius as a last column. 
Or, in case you know how to use VTK, manipulate the vtkPolyData containing centerlines directly.
Best,

Luca


On Aug 7, 2013, at 6:09 PM, Nikhil Paliwal wrote:

> Hi,
> Is there a command in vmtk which will give me the radius and the center of the largest possible sphere within my vessel(stl file)? It would be okay if the sphere touches the vessel, but it should not go out of it.
> Thanks
> Nikhil
> 
> -- 
> Nikhil Paliwal
> PhD Candidate
> Department of Mechanical Engineering
> University at Buffalo
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite!
> It's a free troubleshooting tool designed for production.
> Get down to code-level detail for bottlenecks, with <2% overhead. 
> Download for free and get started troubleshooting in minutes. 
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk_______________________________________________
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[vmtk-users] Maximum inscribed sphere radius

[Nikhil Paliwal <npaliwal@bu...>]

Hi,
Is there a command in vmtk which will give me the radius and the center of
the largest possible sphere within my vessel(stl file)? It would be okay if
the sphere touches the vessel, but it should not go out of it.
Thanks
Nikhil

-- 
Nikhil Paliwal
PhD Candidate
Department of Mechanical Engineering
University at Buffalo