vmtk-users

Re: [vmtk-users] How to use vmtk in c++?

[Luca A. <luc...@gm...>]

Hello Haibin,
 vmtk is composed of a low-level layer in C++ and a high-level layer in Python (www.python.org).
A vmtk pipe is essentially a Python program that you compose at the command line.

Therefore, you'll be able to run a pipe outside of PypePad, you just need to run it inside any
Python interpreter.

However, if you need to use vmtk functionality from C++ you need to use vmtk C++ classes 
directly, such as vtkvmtkPolyDataCenterlines. These are all classes derived from VTK classes,
so the best way to learn how to use vmtk from C++ is to learn VTK (www.vtk.org).

You can find all C++ classes in the vtkVmtk directory and you can have an idea on how to 
use them by looking at how they are instantiated inside the vmtk scripts in the vmtkScripts 
directory.

Hope this gives you an outlook so you can take an informed decision.


Luca



On Apr 22, 2013, at 5:40 PM, Haibin Cai wrote:

> Hello vmtk-users,
>    I can use vmtk to compute the centerlines of vessels now. The only thing I need to do is to type the following in pypepad ---"vmtkcenterlines -ifile E:\\zbuild\\fengeguli.vtp -ofile E:\\zbuild\\fengegulicenter_4.vtp --pipe vmtkrenderer --pipe vmtksurfaceviewer -ifile E:\\zbuild\\fengeguli.vtp -opacity 0.25 --pipe vmtksurfaceviewer -ifile E:\\zbuild\\fengegulicenter_4.vtp".  Is there a way that the program can be operated in vs2010 but not on the pypepad?
> Thanks,
> haibin
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
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[vmtk-users] How to use vmtk in c++?

[Haibin C. <jlc...@gm...>]

Hello vmtk-users,
   I can use vmtk to compute the centerlines of vessels now. The only thing
I need to do is to type the following in pypepad ---"vmtkcenterlines -ifile
E:\\zbuild\\fengeguli.vtp -ofile E:\\zbuild\\fengegulicenter_4.vtp --pipe
vmtkrenderer --pipe vmtksurfaceviewer -ifile E:\\zbuild\\fengeguli.vtp
-opacity 0.25 --pipe vmtksurfaceviewer -ifile
E:\\zbuild\\fengegulicenter_4.vtp".  Is there a way that the program can be
operated in vs2010 but not on the pypepad?
Thanks,
haibin

Re: [vmtk-users] [help!] glibc error

[sipi <si...@gm...>]

Hi Chiara,

Regarding your glibc error.

After a clean install, I had similar problems. However, changing the VTK
GIT_TAG in SuperBuild.cmake from "v5.10.0" back to GIT_TAG "v5.8.0" seems
to be a (temporary) fix.

Best regards,
Joris

Re: [vmtk-users] How to improve the computing of centerlines?

[Luca A. <luc...@gm...>]

Hello Haibin,
 the issue is very likely not "near" or "far", but the fact that your distal vessels are very thin compared to the 
surface triangle resolution. This causes the Voronoi diagram to degenerate and the centerline backtracking 
to fail.

The workaround in these cases is to use 
vmtksurfacesubdivision -method loop
prior to centerline computation in order to artificially increase the resolution of the surface.

If the number of triangles becomes very large after subdividing, you can add a decimate step, making it become

vmtksurfacesubdivision -method loop -ifile foo.vtp --pipe vmtksurfacedecimation -reduction 0.5 --pipe vmtkcenterlines ...

Hope this helps.

Luca



On Apr 20, 2013, at 4:22 AM, Haibin Cai wrote:

> Dear vmtkusers,
>    I have a problem of  computing centerlines when I position one soure point and one target point. If the target point is comparative near, it works well. But when I put the target point comparative far, it start from other point. It seems that the branch is not connected. Furthermore, there is three warnings:
> 
> Generic Warning: In C:\Users\orobix\Documents\VMTK\vmtk-build\VTK\Common\vtkMath.cxx, line 553
> Unable to factor linear system
> 
> Warning: In C:\Users\orobix\Documents\VMTK\vmtk-build\VTK\Graphics\vtkDelaunay3D.cxx, line 487
> vtkDelaunay3D (0311A688): 149 degenerate triangles encountered, mesh quality suspect
> 
> Warning: In C:\Users\orobix\Documents\VMTK\vmtk\vtkVmtk\ComputationalGeometry\vtkvmtkSteepestDescentLineTracer.cxx, line 231
> vtkvmtkSteepestDescentLineTracer (09FC28B0): Degenerate descent detected. Target not reached.
> Here is the result
> <1.jpg><2.jpg>
> What does the warning mean? What should I do to let the centerline reach the real target point? 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
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> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] vmtkApps?

[Luca A. <luc...@or...>]

Hello Evan,
 at the present stage you can download them from github.com/vmtk/vmtk

If you don't use git, just get the source code zip at

https://github.com/vmtk/vmtk/archive/master.zip

and unpack. vmtkApps contains the Python scripts you're looking for.

Best,

Luca


On Apr 20, 2013, at 12:09 AM, Evan Kao wrote:

> Hello vmtk-users,
> 
> I'm interested in going through the parent vessel reconstruction tutorial but I don't think I have the relevant Python scripts.  The tutorial says the files are in the vmtkApps folder, but I couldn't find anything like that.  Are they usually included in the installation?  Where could I find these scripts (and possibly other vmtkApps)?
> 
> Thank you,
> Evan Kao 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] Erro with Parent vessel reconstruction

[Luca A. <luc...@or...>]

Hi Edwin,
 it looks like an issue following the computation of centerlines,
but I can't tell what it is (the warning you mention is in general innocuous).
Please send the surface over, we'll take a look at it.

Luca


On Apr 16, 2013, at 6:16 PM, ed...@el... wrote:

> Hello Luca:
> I try to use the Parent vessel reconstruction with a test surface but i
> have this warning in many times: vtkMath.cxx, line 553 Unable to factor
> linear system, then the program crash.
> Can you help me please, i can send the surface test, if you want.
> 
> Thanks,
> 
> Edwin Maldonado T
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] vmtkApps?

[Evan K. <to...@gm...>]

Hello vmtk-users,

I'm interested in going through the parent vessel reconstruction tutorial
but I don't think I have the relevant Python scripts.  The tutorial says
the files are in the vmtkApps folder, but I couldn't find anything like
that.  Are they usually included in the installation?  Where could I find
these scripts (and possibly other vmtkApps)?

Thank you,
Evan Kao

Re: [vmtk-users] Problem of reading DICOM images to VMTK

[Vincent Ip <drv...@gm...>]

Dear Luca,

It works!!!!

Many thanks!

Vincent

On Apr 18, 2013, at 11:46 PM, Luca Antiga <luc...@gm...> wrote:

> Hi Vincent,
>  please try with 
> 
> vmtkimageviewer -ifile file_path
> 
> where file_path is the path to the first dicom file in your series.
> 
> Let us know.
> 
> Luca
> 
> 
> On Apr 19, 2013, at 1:47 AM, Vincent Ip wrote:
> 
>> Dear VMTK users,
>> 
>> I have a problem of loading DICOM images into VMTK and I'm not sure what is the problem.
>> 
>> I normally export the series of DICOM images (mainly TOF in a MRA series) from OsiriX to a folder with a flat folder tree and without modifying the file compression. (Actually I tried both decompress and not modifying it at all)
>> 
>> Then I load it to VMTK with the following syntax:
>> vmtkimagereader -f dicom -d dicom_directory_path --pipe vmtkimageviewer
>> 
>> But what I got is this image:
>> 
>> <Screen Shot 2013-04-18 at 4.41.02 PM.png>
>> 
>> Anyone has clue on this??
>> 
>> Thanks,
>> Vincent
>> ------------------------------------------------------------------------------
>> Precog is a next-generation analytics platform capable of advanced
>> analytics on semi-structured data. The platform includes APIs for building
>> apps and a phenomenal toolset for data science. Developers can use
>> our toolset for easy data analysis & visualization. Get a free account!
>> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 

Re: [vmtk-users] Problem of reading DICOM images to VMTK

[Luca A. <luc...@gm...>]

Hi Vincent,
 please try with 

vmtkimageviewer -ifile file_path

where file_path is the path to the first dicom file in your series.

Let us know.

Luca


On Apr 19, 2013, at 1:47 AM, Vincent Ip wrote:

> Dear VMTK users,
> 
> I have a problem of loading DICOM images into VMTK and I'm not sure what is the problem.
> 
> I normally export the series of DICOM images (mainly TOF in a MRA series) from OsiriX to a folder with a flat folder tree and without modifying the file compression. (Actually I tried both decompress and not modifying it at all)
> 
> Then I load it to VMTK with the following syntax:
> vmtkimagereader -f dicom -d dicom_directory_path --pipe vmtkimageviewer
> 
> But what I got is this image:
> 
> <Screen Shot 2013-04-18 at 4.41.02 PM.png>
> 
> Anyone has clue on this??
> 
> Thanks,
> Vincent
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] Problem of reading DICOM images to VMTK

[Vincent Ip <drv...@gm...>]

Dear VMTK users,

I have a problem of loading DICOM images into VMTK and I'm not sure what is the problem.

I normally export the series of DICOM images (mainly TOF in a MRA series) from OsiriX to a folder with a flat folder tree and without modifying the file compression. (Actually I tried both decompress and not modifying it at all)

Then I load it to VMTK with the following syntax:
vmtkimagereader -f dicom -d dicom_directory_path --pipe vmtkimageviewer

But what I got is this image:



Anyone has clue on this??

Thanks,
Vincent

[vmtk-users] Erro with Parent vessel reconstruction

[<ed...@el...>]

Hello Luca:
I try to use the Parent vessel reconstruction with a test surface but i
have this warning in many times: vtkMath.cxx, line 553 Unable to factor
linear system, then the program crash.
Can you help me please, i can send the surface test, if you want.

Thanks,

Edwin Maldonado T

Re: [vmtk-users] Beginner question

[Luca A. <luc...@gm...>]

Hi Vincent,
 what I would do to try to understand what goes wrong is to try simplifying the
process: in the second pipe, set -boundarylayer 0, then just write out as msh directly after scaling:

vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 0 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu --pipe vmtkmeshscaling -scale 0.1 --pipe vmtkmeshwriter -entityidsarray CellEntityIds -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh

Let's see what this produces.


Luca



--
Luca Antiga, PhD
Cofounder and Principal Scientist, Orobix Srl
via L.A. Muratori 3, 24123 Bergamo, Italy

orobix: www.orobix.com
home: lantiga.github.com
twitter: twitter.com/lantiga

On Apr 12, 2013, at 7:56 PM, Vincent Ip wrote:

> And when I tried to open it with Fluent, it shows the following error messages:
> 
> > Reading "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh"...
>   563043 nodes.
>    94612 mixed wall faces, zone  3.
>      476 mixed wall faces, zone  4.
>      456 mixed wall faces, zone  5.
>      464 mixed wall faces, zone  6.
> Error: read: face 5234350, zone 7.
> Reading Faces: failed while reading section 13.
> 
>        Clearing partially read grid.
> 
> Error: Read_Grid_Section: Aborted due to critical error.
> Error Object: #f
> 
> Error: Error reading "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh".
> Error Object: #f
> 
> Interrupting...
> Done.
> 
> Vincent
> 
> On Apr 12, 2013, at 10:01 AM, Vincent Ip <drv...@gm...> wrote:
> 
>> Thanks Luca for your prompt response!
>> 
>> Here are the command lines I used:
>> 
>> vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkflowextensions -adaptivelength 1 -extensionratio 20 -normalestimationratio 1 -interactive 0 -extensionmode boundarynormal --pipe vmtksurfacewriter -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp
>> 
>> vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu
>> 
>> vmtklineartoquadratic -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -rfile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp -entityidsarray CellEntityIds
>> 
>> vmtkmeshscaling -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -scale 0.1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu
>> 
>> vmtkmeshboundaryinspector -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -entityidsarray CellEntityIds
>> 
>> vmtkmeshtetrahedralize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu
>> 
>> vmtkmeshlinearize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu
>> 
>> vmtkmeshwriter -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu -entityidsarray CellEntityIds -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh
>> 
>> And I am currently using MacOS 10.8.3 and my laptop is a 2.7GHz quad-core with 16GB ram. And I am using ANSYS 14.0.
>> 
>> Please kindly advise on what steps should I follow for subsequent processing.
>> Many many thanks indeed.
>> 
>> Vincent
>> 
>> On Apr 12, 2013, at 3:56 AM, Luca Antiga <luc...@gm...> wrote:
>> 
>>> Hi Vincent,
>>>  for the future please keep messages on the list. I'm not the only 
>>> one that can solve your problem, by posting on the list you have 
>>> better chances to get useful feedback in shorter times.
>>> 
>>> Hey, relax! No need to be desperate. Things can be tricky at the 
>>> beginning as there is a learning curve, but you'll be ok soon.
>>> 
>>> I personally don't think the model is odd. The orientation of 
>>> the flow extensions is debatable (vmtk tries to take a representative
>>> direction of the vessel upstream the end section, but it can generate
>>> non particularly representative extensions in the case there are
>>> high curvatures near the end section, as in your case). You can
>>> try with 
>>> -extensionmode boundarynormal
>>> for extensions that have the direction of the normal to the boundary,
>>> and see what happens.
>>> 
>>> In any case, I don't think the direction is odd enough to cause troubles,
>>> so let's see the mesh. Can you send me the exact command line you
>>> used to generate the mesh all the way to the generation of the msh
>>> file?
>>> 
>>> 
>>> Luca
>>> 
>>> 
>>> On Apr 12, 2013, at 8:45 AM, Vincent Ip wrote:
>>> 
>>>> Thanks Luca,
>>>> 
>>>> I almost cried when I saw your email. You have no idea how desperate I am right now.
>>>> Alright, I've attached a picture of what did I mean the model is odd after adding the flow extension.
>>>> Please kindly comment.
>>>> Many thanks!!!
>>>> 
>>>> Vincent
>>>> 
>>>> <PastedGraphic-1.tiff>
>>>> On Apr 11, 2013, at 11:36 PM, Luca Antiga <luc...@gm...> wrote:
>>>> 
>>>>> Hi Vincent,
>>>>> welcome to vmtk.
>>>>> In order to help you we need some more information about what's the actual issue you're coming across. Let's start with your first question: can you post a screenshot?
>>>>> Cheers
>>>>> 
>>>>> Luca
>>>>> 
>>>>> On 12/apr/2013, at 08:15, Vincent Ip <drv...@gm...> wrote:
>>>>> 
>>>>>> I am a new beginner in learning how to reconstruct blood vessel from MR angiogram source image for CFD analysis.
>>>>>> 
>>>>>> I followed the VMTK tutorial step by step to reconstruct the middle cerebral artery and then export it to mesh for FLUENT. But it just doesn't work!
>>>>>> 
>>>>>> I have a few questions that I don't understand and I really hope someone could show me some guidances (I'm really desperate!!)
>>>>>> - After adding the flow extension, the mesh seems a bit odd and it doesn't look like the one which is depicted as an example on the page of 'generating a mesh'. Is it really necessary to make it or anything I missed to do during the meshing
>>>>>> - And the *.msh file generated (for Fluent) is not readable by Fluent
>>>>>> - I tried the netgen way but I don't know how to use it
>>>>>> 
>>>>>> I am not sure what did I do wrong but I would appreciate if anyone could advise me on how to generate a proper CFD model from MRA.
>>>>>> Many thanks in advance.
>>>>>> 
>>>>>> Vincent
>>>>>> ------------------------------------------------------------------------------
>>>>>> Precog is a next-generation analytics platform capable of advanced
>>>>>> analytics on semi-structured data. The platform includes APIs for building
>>>>>> apps and a phenomenal toolset for data science. Developers can use
>>>>>> our toolset for easy data analysis & visualization. Get a free account!
>>>>>> http://www2.precog.com/precogplatform/slashdotnewsletter
>>>>>> _______________________________________________
>>>>>> vmtk-users mailing list
>>>>>> vmt...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>> 
>>> 
>> 
> 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] how to display two surface together in vmtk?

[Simone M. <sim...@or...>]

Dear Haibin,
Use the vmtkrenderer script and then vmtksurfaceviewer for each surface.
You can set opacity in case the second surface is inside the first one (for example a centerline)

vmtkrenderer --pipe vmtksurfaceviewer -ifile sup1.vtp -opacity 0.25 --pipe vmtksurfaceviewer -ifile sup2.vtp

Press 'q' to go further to the second rendering.

Simone

--
Simone Manini, Eng
Orobix Srl
via L.A. Muratori 3, 24123 Bergamo, Italy

orobix: www.orobix.com
home: http://daron1337.github.com
twitter: twitter.com/daron1337
mobile:	+39.328.60.22.017
office:	+39.035.0296480
		+39.035.42131

"This message originates from Orobix Srl and its contents and attachments are privileged and confidential and are intended only for the individual(s) or entity(ies) named above. This message should not be forwarded, distributed or disclosed. Any unauthorized use, dissemination and duplication is strictly prohibited and may be unlawful. All personal messages express views solely of the sender, which are not to be attributed to Orobix Srl, and may not be copied or distributed without this disclaimer. If you are not the intended recipient or received this message in error, please delete this message and notify the sender by reply e-mail. Opinions, conclusions and other information in this message that do not relate to the official business of Orobix Srl shall be understood as neither given nor endorsed by it."

On Apr 15, 2013, at 2:57 PM, Haibin Cai <jlc...@gm...> wrote:

> Dear vmtkusers,
>     I want to display two surface together in vmtk. The command of "vmtksurfacereader -ifile foo1.vtp --pipe vmtksurfacereader -ifile foo2.vtp --pipe vmtksurfaceiviewer"  can only display the second surface. Does there exist anyway that I can show them together?
> Thanks
> haibin
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] how to display two surface together in vmtk?

[Haibin C. <jlc...@gm...>]

Dear vmtkusers,
    I want to display two surface together in vmtk. The command of
"vmtksurfacereader
-ifile foo1.vtp --pipe vmtksurfacereader -ifile foo2.vtp --pipe
vmtksurfaceiviewer"  can only display the second surface. Does there exist
anyway that I can show them together?
Thanks
haibin

Re: [vmtk-users] how to compute centerlines when there is a branch?

[Simone M. <sim...@or...>]

Dear Haibin,
In order to compute centerlines for vessels with more than one branch it is sufficient to select one source point and a then a destination point for each branch.

Simone

--
Simone Manini, Eng
Orobix Srl
via L.A. Muratori 3, 24123 Bergamo, Italy

orobix: www.orobix.com
home: http://daron1337.github.com
twitter: twitter.com/daron1337
mobile:	+39.328.60.22.017
office:	+39.035.0296480
		+39.035.42131

"This message originates from Orobix Srl and its contents and attachments are privileged and confidential and are intended only for the individual(s) or entity(ies) named above. This message should not be forwarded, distributed or disclosed. Any unauthorized use, dissemination and duplication is strictly prohibited and may be unlawful. All personal messages express views solely of the sender, which are not to be attributed to Orobix Srl, and may not be copied or distributed without this disclaimer. If you are not the intended recipient or received this message in error, please delete this message and notify the sender by reply e-mail. Opinions, conclusions and other information in this message that do not relate to the official business of Orobix Srl shall be understood as neither given nor endorsed by it."

On Apr 14, 2013, at 4:50 PM, Haibin Cai <jlc...@gm...> wrote:

> Dear vmtkusers,
>     I have just compute the centerline of a vessel that has no branch with the help of "http://www.vmtk.org/Tutorials/Centerlines/". I position one soure point and one target point, than the centerline  is computed. However I want to acquire the centerlines of the vessel which has two branches. What should I do?
> Thanks
> haibin
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] how to compute centerlines when there is a branch?

[Haibin C. <jlc...@gm...>]

Dear vmtkusers,
    I have just compute the centerline of a vessel that has no branch with
the help of "http://www.vmtk.org/Tutorials/Centerlines/". I position one
soure point and one target point, than the centerline  is computed. However
I want to acquire the centerlines of the vessel which has two branches.
What should I do?
Thanks
haibin

Re: [vmtk-users] Beginner question

[Vincent Ip <drv...@gm...>]

And when I tried to open it with Fluent, it shows the following error messages:

> Reading "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh"...
  563043 nodes.
   94612 mixed wall faces, zone  3.
     476 mixed wall faces, zone  4.
     456 mixed wall faces, zone  5.
     464 mixed wall faces, zone  6.
Error: read: face 5234350, zone 7.
Reading Faces: failed while reading section 13.

       Clearing partially read grid.

Error: Read_Grid_Section: Aborted due to critical error.
Error Object: #f

Error: Error reading "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh".
Error Object: #f

Interrupting...
Done.

Vincent

On Apr 12, 2013, at 10:01 AM, Vincent Ip <drv...@gm...> wrote:

> Thanks Luca for your prompt response!
> 
> Here are the command lines I used:
> 
> vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkflowextensions -adaptivelength 1 -extensionratio 20 -normalestimationratio 1 -interactive 0 -extensionmode boundarynormal --pipe vmtksurfacewriter -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp
> 
> vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu
> 
> vmtklineartoquadratic -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -rfile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp -entityidsarray CellEntityIds
> 
> vmtkmeshscaling -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -scale 0.1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu
> 
> vmtkmeshboundaryinspector -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -entityidsarray CellEntityIds
> 
> vmtkmeshtetrahedralize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu
> 
> vmtkmeshlinearize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu
> 
> vmtkmeshwriter -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu -entityidsarray CellEntityIds -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh
> 
> And I am currently using MacOS 10.8.3 and my laptop is a 2.7GHz quad-core with 16GB ram. And I am using ANSYS 14.0.
> 
> Please kindly advise on what steps should I follow for subsequent processing.
> Many many thanks indeed.
> 
> Vincent
> 
> On Apr 12, 2013, at 3:56 AM, Luca Antiga <luc...@gm...> wrote:
> 
>> Hi Vincent,
>>  for the future please keep messages on the list. I'm not the only 
>> one that can solve your problem, by posting on the list you have 
>> better chances to get useful feedback in shorter times.
>> 
>> Hey, relax! No need to be desperate. Things can be tricky at the 
>> beginning as there is a learning curve, but you'll be ok soon.
>> 
>> I personally don't think the model is odd. The orientation of 
>> the flow extensions is debatable (vmtk tries to take a representative
>> direction of the vessel upstream the end section, but it can generate
>> non particularly representative extensions in the case there are
>> high curvatures near the end section, as in your case). You can
>> try with 
>> -extensionmode boundarynormal
>> for extensions that have the direction of the normal to the boundary,
>> and see what happens.
>> 
>> In any case, I don't think the direction is odd enough to cause troubles,
>> so let's see the mesh. Can you send me the exact command line you
>> used to generate the mesh all the way to the generation of the msh
>> file?
>> 
>> 
>> Luca
>> 
>> 
>> On Apr 12, 2013, at 8:45 AM, Vincent Ip wrote:
>> 
>>> Thanks Luca,
>>> 
>>> I almost cried when I saw your email. You have no idea how desperate I am right now.
>>> Alright, I've attached a picture of what did I mean the model is odd after adding the flow extension.
>>> Please kindly comment.
>>> Many thanks!!!
>>> 
>>> Vincent
>>> 
>>> <PastedGraphic-1.tiff>
>>> On Apr 11, 2013, at 11:36 PM, Luca Antiga <luc...@gm...> wrote:
>>> 
>>>> Hi Vincent,
>>>> welcome to vmtk.
>>>> In order to help you we need some more information about what's the actual issue you're coming across. Let's start with your first question: can you post a screenshot?
>>>> Cheers
>>>> 
>>>> Luca
>>>> 
>>>> On 12/apr/2013, at 08:15, Vincent Ip <drv...@gm...> wrote:
>>>> 
>>>>> I am a new beginner in learning how to reconstruct blood vessel from MR angiogram source image for CFD analysis.
>>>>> 
>>>>> I followed the VMTK tutorial step by step to reconstruct the middle cerebral artery and then export it to mesh for FLUENT. But it just doesn't work!
>>>>> 
>>>>> I have a few questions that I don't understand and I really hope someone could show me some guidances (I'm really desperate!!)
>>>>> - After adding the flow extension, the mesh seems a bit odd and it doesn't look like the one which is depicted as an example on the page of 'generating a mesh'. Is it really necessary to make it or anything I missed to do during the meshing
>>>>> - And the *.msh file generated (for Fluent) is not readable by Fluent
>>>>> - I tried the netgen way but I don't know how to use it
>>>>> 
>>>>> I am not sure what did I do wrong but I would appreciate if anyone could advise me on how to generate a proper CFD model from MRA.
>>>>> Many thanks in advance.
>>>>> 
>>>>> Vincent
>>>>> ------------------------------------------------------------------------------
>>>>> Precog is a next-generation analytics platform capable of advanced
>>>>> analytics on semi-structured data. The platform includes APIs for building
>>>>> apps and a phenomenal toolset for data science. Developers can use
>>>>> our toolset for easy data analysis & visualization. Get a free account!
>>>>> http://www2.precog.com/precogplatform/slashdotnewsletter
>>>>> _______________________________________________
>>>>> vmtk-users mailing list
>>>>> vmt...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>> 
>> 
> 

Re: [vmtk-users] Beginner question

[Vincent Ip <drv...@gm...>]

Thanks Luca for your prompt response!

Here are the command lines I used:

vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkflowextensions -adaptivelength 1 -extensionratio 20 -normalestimationratio 1 -interactive 0 -extensionmode boundarynormal --pipe vmtksurfacewriter -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp

vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu

vmtklineartoquadratic -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -rfile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp -entityidsarray CellEntityIds

vmtkmeshscaling -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -scale 0.1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu

vmtkmeshboundaryinspector -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -entityidsarray CellEntityIds

vmtkmeshtetrahedralize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu

vmtkmeshlinearize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu

vmtkmeshwriter -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu -entityidsarray CellEntityIds -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh

And I am currently using MacOS 10.8.3 and my laptop is a 2.7GHz quad-core with 16GB ram. And I am using ANSYS 14.0.

Please kindly advise on what steps should I follow for subsequent processing.
Many many thanks indeed.

Vincent

On Apr 12, 2013, at 3:56 AM, Luca Antiga <luc...@gm...> wrote:

> Hi Vincent,
>  for the future please keep messages on the list. I'm not the only 
> one that can solve your problem, by posting on the list you have 
> better chances to get useful feedback in shorter times.
> 
> Hey, relax! No need to be desperate. Things can be tricky at the 
> beginning as there is a learning curve, but you'll be ok soon.
> 
> I personally don't think the model is odd. The orientation of 
> the flow extensions is debatable (vmtk tries to take a representative
> direction of the vessel upstream the end section, but it can generate
> non particularly representative extensions in the case there are
> high curvatures near the end section, as in your case). You can
> try with 
> -extensionmode boundarynormal
> for extensions that have the direction of the normal to the boundary,
> and see what happens.
> 
> In any case, I don't think the direction is odd enough to cause troubles,
> so let's see the mesh. Can you send me the exact command line you
> used to generate the mesh all the way to the generation of the msh
> file?
> 
> 
> Luca
> 
> 
> On Apr 12, 2013, at 8:45 AM, Vincent Ip wrote:
> 
>> Thanks Luca,
>> 
>> I almost cried when I saw your email. You have no idea how desperate I am right now.
>> Alright, I've attached a picture of what did I mean the model is odd after adding the flow extension.
>> Please kindly comment.
>> Many thanks!!!
>> 
>> Vincent
>> 
>> <PastedGraphic-1.tiff>
>> On Apr 11, 2013, at 11:36 PM, Luca Antiga <luc...@gm...> wrote:
>> 
>>> Hi Vincent,
>>> welcome to vmtk.
>>> In order to help you we need some more information about what's the actual issue you're coming across. Let's start with your first question: can you post a screenshot?
>>> Cheers
>>> 
>>> Luca
>>> 
>>> On 12/apr/2013, at 08:15, Vincent Ip <drv...@gm...> wrote:
>>> 
>>>> I am a new beginner in learning how to reconstruct blood vessel from MR angiogram source image for CFD analysis.
>>>> 
>>>> I followed the VMTK tutorial step by step to reconstruct the middle cerebral artery and then export it to mesh for FLUENT. But it just doesn't work!
>>>> 
>>>> I have a few questions that I don't understand and I really hope someone could show me some guidances (I'm really desperate!!)
>>>> - After adding the flow extension, the mesh seems a bit odd and it doesn't look like the one which is depicted as an example on the page of 'generating a mesh'. Is it really necessary to make it or anything I missed to do during the meshing
>>>> - And the *.msh file generated (for Fluent) is not readable by Fluent
>>>> - I tried the netgen way but I don't know how to use it
>>>> 
>>>> I am not sure what did I do wrong but I would appreciate if anyone could advise me on how to generate a proper CFD model from MRA.
>>>> Many thanks in advance.
>>>> 
>>>> Vincent
>>>> ------------------------------------------------------------------------------
>>>> Precog is a next-generation analytics platform capable of advanced
>>>> analytics on semi-structured data. The platform includes APIs for building
>>>> apps and a phenomenal toolset for data science. Developers can use
>>>> our toolset for easy data analysis & visualization. Get a free account!
>>>> http://www2.precog.com/precogplatform/slashdotnewsletter
>>>> _______________________________________________
>>>> vmtk-users mailing list
>>>> vmt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> 
> 

Re: [vmtk-users] Beginner question

[Luca A. <luc...@gm...>]

Hi Vincent,
 welcome to vmtk.
In order to help you we need some more information about what's the actual issue you're coming across. Let's start with your first question: can you post a screenshot?
Cheers

Luca

On 12/apr/2013, at 08:15, Vincent Ip <drv...@gm...> wrote:

> I am a new beginner in learning how to reconstruct blood vessel from MR angiogram source image for CFD analysis.
> 
> I followed the VMTK tutorial step by step to reconstruct the middle cerebral artery and then export it to mesh for FLUENT. But it just doesn't work!
> 
> I have a few questions that I don't understand and I really hope someone could show me some guidances (I'm really desperate!!)
> - After adding the flow extension, the mesh seems a bit odd and it doesn't look like the one which is depicted as an example on the page of 'generating a mesh'. Is it really necessary to make it or anything I missed to do during the meshing
> - And the *.msh file generated (for Fluent) is not readable by Fluent
> - I tried the netgen way but I don't know how to use it
> 
> I am not sure what did I do wrong but I would appreciate if anyone could advise me on how to generate a proper CFD model from MRA.
> Many thanks in advance.
> 
> Vincent
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] Beginner question

[Vincent Ip <drv...@gm...>]

I am a new beginner in learning how to reconstruct blood vessel from MR angiogram source image for CFD analysis.

I followed the VMTK tutorial step by step to reconstruct the middle cerebral artery and then export it to mesh for FLUENT. But it just doesn't work!

I have a few questions that I don't understand and I really hope someone could show me some guidances (I'm really desperate!!)
- After adding the flow extension, the mesh seems a bit odd and it doesn't look like the one which is depicted as an example on the page of 'generating a mesh'. Is it really necessary to make it or anything I missed to do during the meshing
- And the *.msh file generated (for Fluent) is not readable by Fluent
- I tried the netgen way but I don't know how to use it

I am not sure what did I do wrong but I would appreciate if anyone could advise me on how to generate a proper CFD model from MRA.
Many thanks in advance.

Vincent

Re: [vmtk-users] vmtkmeshprojection

[Luca A. <luc...@or...>]

Hi Lucia,
 correct, it's a simple linear interpolation. 
vmtk contains all the infrastructure for doing more sophisticated
L2 projections, but I've never really needed it so far apart from a
few very specific projects, so it's not exposed at the script level.
Best,

Luca


On Apr 10, 2013, at 6:15 AM, Lucia Mirabella wrote:

> Hi Luca,
> 
> I'm using vmtkmeshprojection to project some data from one mesh to another one and I would like to know which method it is used to do so (to be able to reference it and describe it). Is it a linear interpolation?
> 
> Thank you!
> 
> Lucia
> 
> __________________________________________________
> 
> Postdoctoral Fellow, Cardiovascular Fluid Mechanics Laboratory
> Wallace H. Coulter Department of Biomedical Engineering
> Georgia Institute of Technology
> 315 Ferst Drive NW, Parker H. Petit Biotechnology Building
> Atlanta, GA 30332-0363
> E-mail: luc...@bm...
> 
> 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] vmtkmeshprojection

[Lucia M. <lmi...@ma...>]

Hi Luca,

I'm using vmtkmeshprojection to project some data from one mesh to another one and I would like to know which method it is used to do so (to be able to reference it and describe it). Is it a linear interpolation?

Thank you!

Lucia

__________________________________________________

Postdoctoral Fellow, Cardiovascular Fluid Mechanics Laboratory
Wallace H. Coulter Department of Biomedical Engineering
Georgia Institute of Technology
315 Ferst Drive NW, Parker H. Petit Biotechnology Building
Atlanta, GA 30332-0363
E-mail: luc...@bm...

Re: [vmtk-users] How to calculate the ICA angle or planarity angle in VMTK or Paraview

[Luca A. <luc...@or...>]

Hi YiQiang,
 there was not attachment. In any case, I confirm that the bifurcation vector corresponding to group 0 is the CCA vector.
What you wrote is correct.
Best,

Luca


On Apr 5, 2013, at 6:32 PM, qiang zeng wrote:

> Hi Luca,
> From the file (as an attachment, vmtk.jpg), the bifurcation angle is the differnce between ICA vector and ECA vector projected onto the bifurcation plane. and the ICA angle is the difference between ICA vector and bifurcation vector (that is CCA vector?) projected onto the bifurcation plane.
>  
> the planarity angle is between the out-of-plane of the CCA and ICA vectors.
> Best,
> 
> --- 13年4月2日，周二, Luca Antiga <luc...@or...> 写道：
> 
> 发件人: Luca Antiga <luc...@or...>
> 主题: Re: [vmtk-users] How to calculate the ICA angle or planarity angle in VMTK or Paraview
> 收件人: "qiang zeng" <zen...@ya...>
> 日期: 2013年4月2日,周二,上午4:45
> 
> Hi YiQiang,
> 
> 
>> 1)what difference are between InPlaneBifurcationVectorAngles and  ICA angle?
> 
> The InPlaneBifurcationVectorAngles are the angles between the up-normal vector and a branch vector projected onto the bifurcation plane.
> The ICA angle is the angle between the ICA and ECA vectors projected onto the bifurcation plane. So, by summing the angle between the ICA branch vector and the up-normal and the ECA branch vector and the up-normal you get the ICA angle. Note: here I wrote "sum" because I'm referring to the angles absolute value, but it's really the difference of the signed angles (since the ICA branch and the ECA branch are on opposite sides of the bifurcation up-normal, so one angle will come out positive and the other negative, by the convention used in vmtk).
> 
> The reason why we don't spit the ICA angle directly is just our wish to make the tool generic and not specific to the carotid bifurcation.
> 
>> 2)in the result of the vector (BifurcationVectors, InPlaneBifurcationVectors, OutOfPlaneBifurcationVectors) by VMTK (as an attachment), each part has three groups. and how to get the angle from the vector by VMTK? or do i need to use the other tools (such as Paraview) to caculate the angle value.
> 
> You get both vectors and angles. In fact, the InPlaneBifurcationVectorAngles are angles in radians, while the InPlaneBifurcationVectors are the vector components from which the angle is computed.
> 
>> 3)for the ICA angle, i need to get the difference between the two downstream inplane angles. but the InPlaneBifurcationVectors has two downstream groups vector [(--0.27,0.18,2.60), (0.60, -0.50.0.89)] and how to distinguish and control these vectors.
> 
> You should look at the InPlaneBifurcationVectorAngles and take the difference (see point above) between the angles for group 2 and 3 (which correspond to the ICA and ECA - assuming you selected the output target point of the ICA as first when extracting centerlines).
> 
> So, in your case, ICA = 0.26687 - (- 0.608927) = 0.875797 (in radians) = 50.18 (in degrees)
> 
> Hope this clarifies it.
> 
> 
> Luca
> 
> 
> 
> On Mar 29, 2013, at 4:20 PM, qiang zeng wrote:
> 
>> Hi Luca,
>> Thank you for your reply.
>> I have already saw the "Computing bifurcation geometry" section. but i have some doubt:
>> 1)what difference are between InPlaneBifurcationVectorAngles and  ICA angle?
>> 2)in the result of the vector (BifurcationVectors, InPlaneBifurcationVectors, OutOfPlaneBifurcationVectors) by VMTK (as an attachment), each part has three groups. and how to get the angle from the vector by VMTK? or do i need to use the other tools (such as Paraview) to caculate the angle value.
>> 3)for the ICA angle, i need to get the difference between the two downstream inplane angles. but the InPlaneBifurcationVectors has two downstream groups vector [(--0.27,0.18,2.60), (0.60, -0.50.0.89)] and how to distinguish and control these vectors.
>>  
>> Best,
>> YiQiang
>> 
>> 
>> --- 13年3月29日，周五, Luca Antiga <luc...@gm...> 写道：
>> 
>> 发件人: Luca Antiga <luc...@gm...>
>> 主题: Re: [vmtk-users] How to calculate the ICA angle or planarity angle in VMTK or Paraview
>> 收件人: "qiang zeng" <zen...@ya...>
>> 抄送: vmt...@li...
>> 日期: 2013年3月29日,周五,下午9:35
>> 
>> Hi YiQiang,
>>  the angles you get from vmtk are explained in http://www.vmtk.org/Tutorials/GeometricAnalysis/, 
>> "Computing bifurcation geometry" section.
>> 
>> The ICA angle is the difference between the two downstream inplane angles, while the planarity angle
>> is the difference between the upstream and downstream out of plane angles.
>> 
>> Hope this gives you a hint
>> 
>> 
>> Luca
>> 
>> 
>> 
>> On Mar 28, 2013, at 9:10 AM, qiang zeng wrote:
>> 
>>> Dear VMTK users,
>>> In my works, I need to calculate the ICA angle and planarity angle like the Stroke 2005 paper. but I didn't get the result from the Paraview.
>>> Does anyone know a way to do this?
>>> 
>>> Thanks in advance!
>>> Best wishes,
>>> YiQiang Zeng
>>> ------------------------------------------------------------------------------
>>> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
>>> Rise to greatness in Intel's independent game demo contest.
>>> Compete for recognition, cash, and the chance to get your game 
>>> on Steam. $5K grand prize plus 10 genre and skill prizes. 
>>> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
>>> vmtk-users mailing list
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>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> 
>> <data.jpg>
> 
> 
> 
> 
> 
> 
> 
> 

Re: [vmtk-users] Level set segmentation references

[Luca A. <luc...@or...>]

Hi Evan,
 the main issue with the data (not your fault) seems to be that images have a strongly anisotropic resolution (thick slice).
The combination between small vessels (of size comparable to the resolution, at least in one direction) and anisotropy
leads to inaccurate image intensity gradients and consequently to weird "motion" of the level set surface.

You can try resampling your image to a more isotropic resolution using a high-order interpolation scheme (such as 
cubic or b-spline). Usually this helps only moderately, but it's worth a try.

What I've done in these situations in the past has been to use a more constrained segmentation, such as polygonal surface 
deformation after Marching Cubes extraction or even deformable tubes (centerline + radius).

The main issue lies in the lack of information in one direction, which you have to make up for someway or another.

Luca


On Apr 5, 2013, at 1:19 AM, Evan Kao wrote:

> Hello Luca,
> 
> Thanks for the references.  As for the specific problem itself, I have attached a couple images (it is an arterviovenous fistula).  I am using dicom data from cine-MR measurements.  When using the suggested settings of [300 0 0 1] during level set segmentation, part of the vessel on the right (vein) does not appear.  Fewer iterations (30-50) seem to do a better job of keeping that segment filled, although it still appears under-filled.  I have tried to get around this by segmenting the two vessels separately, using different parameters for each one.  The process becomes a balancing act between the PropagationScaling and CurvatureScaling parameters (I used [30 1 1 1] for the vein, [200 1 1 1] for the artery to get passable results), and the resulting lumenal geometry feels a little arbitrary.  But more problematic is that I end up having to use the Fast Marching method on the underfilled area to adequately fill it, which ends up hurting the reproducibility of the geometry and kind of defeats the purpose of using level set segmentation over something simpler, like simply eyeballing thresholds with vmtkmarchingcubes.
> 
> Please let me know if you have any suggestions.
> 
> Thanks,
> Evan Kao
> 
> 
> On Fri, Mar 29, 2013 at 5:43 AM, Luca Antiga <luc...@or...> wrote:
> Hi Evan,
> 
> On Mar 22, 2013, at 9:48 PM, Evan Kao wrote:
> 
>> Hello,
>> 
>> I am trying to segment a particular set of 3D-cine images with vmtklevelsetsegmentation, but the perhaps due to the shape of the vessel and/or quality of the images, the suggested settings of 300 0 0 1 isn't working well.  I've tried playing around with the level set deformation parameters, but the resultant shapes feel just as arbitrary as if I had simply used thresholds directly.  Can you recommend any guides or references that can explain in more depth (i.e. quantitatively) how the parameters affect the deformation, and/or also provide an explanation of the additional options available in vmtklevelsetsegmentation that weren't covered in the tutorials?
> 
> The level set parameters are those of itkGeodesicActiveContourLevelSetImageFilter and itkGeodesicActiveContourLevelSetFunction. 
> http://www.itk.org/Doxygen/html/classitk_1_1GeodesicActiveContourLevelSetImageFilter.html
> http://www.itk.org/Doxygen/html/classitk_1_1GeodesicActiveContourLevelSetFunction.html
> 
> The main reference for level set methods is
> J. A. Sethian, "Level Set Methods and Fast Marching Methods", Cambridge University Press, 1996. 
> but you can find a lot of material around.
> 
> You may want to take a look at my PhDThesis (good old times) at lantiga.github.com/about/
> 
> If you have noise issues, I suggest you to use a non-zero featurederivativesigma , which expresses the width of the 
> gaussian kernel used for performing partial derivatives for the feature image. It's expressed in physical spatial units
> (e.g. mm) and it's roughly related to the minimum scale that you'll end up detecting in the image - i.e. the noise below
> that spatial scale is going to be filtered out, thus not affecting the evolution of level sets (again, roughly speaking).
> 
> Feel free to post a couple of screenshots of the problem you're having, so that replies can be more to the point.
> 
> Best,
> 
> Luca
> 
> 
>> Thank you,
>> Evan Kao
>> ------------------------------------------------------------------------------
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> 
> 
> <levelset_300_0_0_1.png><levelset_underfilled2.JPG><levelset_30_0_0_1.JPG><levelset_initialization.JPG><levelset_undefilled.JPG>------------------------------------------------------------------------------
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> the most talented Cisco Certified professionals. Visit the 
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Re: [vmtk-users] Automatically executing VMTK centerline

[Luca A. <luc...@or...>]

Hi Anouk,
 I'm not really sure about what's not working here, the output from vmtk
you attached is not self-explanatory, unfortunately.
Just a note: you shouldn't enclose option values in quotes ('profileidlist')
but just use values unquoted

vmtksurfacereader -ifile H:\Cath_recon_4(1)_10(1)_SC.stl -f stl  --pipe vmtkcenterlines -endpoints 1 -seedselector profileidlist -sourceids 0 -targetids 1 --pipe  vmtkcenterlinegeometry -ofile H:\Cath_recon_4(1)_10(1)_SC_output_testing.dat

Can you try sending more of the text output? Also, does the pipe hang
or just exits successfully without generating a file?

Thanks

Luca


On Apr 3, 2013, at 2:15 PM, Anouk Post wrote:

> Hi Luca,
> 
> You were right, I used idlist instead of profileidlist. 
> 
> Unfortunately, it didn't work, I don't get an output file. 
> 
> INPUT:
> 
> vmtksurfacereader -ifile H:\Cath_recon_4(1)_10(1)_SC.stl -f "stl"  --pipe vmtkcenterlines -endpoints 1 -seedselector 'profileidlist' -sourceids 0 -targetids 1 --pipe  vmtkcenterlinegeometry -ofile H:\Cath_recon_4(1)_10(1)_SC_output_testing.dat
> 
> OUTPUT:
> Image of output is attached (could not copy the text).
> 
> Do you know why it's not working?
> 
> Thanks!
> 
> Best,
> 
> Anouk
> 
> 
> 
> 
> 
> 
> 
> On 29 March 2013 13:28, Luca Antiga <luc...@or...> wrote:
> Hi Anouk,
>  this is what I'd expect from -seedselector idlist, not -seedselector profileidlist.
> Are you sure it was the latter and not the former?
> 
> Luca
> 
> 
> On Mar 29, 2013, at 2:07 PM, Anouk Post wrote:
> 
>> Hi Luca,
>>  
>> I already tried that and it didn't work. It gave me only a partial reconstruction of the centerline (a very short one).
>>  
>> Best,
>>  
>> Anouk
>> 
>> On 29 March 2013 13:04, Luca Antiga <luc...@or...> wrote:
>> Hi Anouk,
>>  try with 
>> -seedselector profileidlist -sourceids 0 -targetids 1
>> 
>> (hoping you have a recent enough version of vmtk)
>> 
>> Best,
>> 
>> 
>> Luca
>> 
>> 
>> On Mar 25, 2013, at 7:36 PM, Anouk Post wrote:
>> 
>>> Dear VMTK users,
>>> 
>>> I am using VMTK centerline to calculate the centerline of an stl file as follows:
>>> 
>>> vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl"  --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe  vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat
>>> 
>>> 
>>> 
>>> For all the different input files I use, the seedselector option always leads to me pressing 'q' '0' '1' and then it works. So I close the viewer, and I think I set the source id as 0 and the target id as 1. 
>>> 
>>> Is there a way to make this an automatic process so I don't have to type q, 0, 1 each time? I've tried using seedselector idlist but I'm not sure how to use it (it does not give me the right answer when I use -sourceids 0 -targetids 1. 
>>> 
>>> Does anyone know a way to do this?
>>> 
>>> 
>>> Thanks in advance!
>>> 
>>> 
>>> Best wishes,
>>> 
>>> 
>>> Anouk
>>> 
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> 
>> 
>> 
>> 
>> -- 
>> Best Wishes,
>> 
>> Anouk
>> ------------------------------------------------------------------------------
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> 
> 
> 
> 
> -- 
> Best Wishes,
> 
> Anouk
> <vmtk.jpg>------------------------------------------------------------------------------
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> Reduce network management and security costs.Learn how to hire 
> the most talented Cisco Certified professionals. Visit the 
> Employer Resources Portal
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