Re: [vmtk-users] not all end-points tracked by vmtkcenterlines
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Re: [vmtk-users] not all end-points tracked by vmtkcenterlines
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From: Richard D. <ric...@ui...> - 2013-03-06 17:44:54
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Luca-- I've been vexed by a similar situation for awhile that I'm just now getting around to tackling. One thing I *do* have, however, is centerlines for my main vessel an all branches. I've noticed a vmtkcenterlinemerge.py/vtkvmtkMergeCenterlines.h/cxx that don't appear to be used anywhere, so I can't find a usage example. What do I need to pass in for the tract ids and blanking ids to make this work, or do you have a usage example somewhere? -rd On 03/04/2013 07:00 AM, Luca Antiga wrote: > Hi Roman, > I'll really need to take a closer look to the data you sent, I'm planning to do it in the next few days. > Thanks > > Luca > > On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote: > >> On 23/02/13 13:56, Luca Antiga wrote: >>> Possible workarounds: >>> >>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily >>> done by specifying -usetetgen 1 in the vmtkcenterlines command line >> Using tetgen I get an error and the resulting VTP-file is empty (second workaround is still running): >> >> Reading VTK XML surface file. >> Executing vmtkcenterlines ... >> Cleaning surface. >> Triangulating surface. >> Computing centerlines. >> Computing centerlines...Running TetGen. >> TetGen command line options: pT1.000000e-08dzQ >> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, line 667 >> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name specified does not exist! >> >> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, line 318 >> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified does not exist! >> >> Done executing vmtkcenterlines. >> Writing VTK XML surface file. >> Output vmtkcenterlines members: >> >>> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi >>> and feed it to vmtkcenterlines, this way: >>> >>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ... >> Using this command causes no errors but the resulting file is also empty. >> >> Any ideas what else I could try? >> >> Many thanks for any help or hints. >> Roman >> >> >> >>> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines) >>> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets. >>> >>> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue. >>> >>> Best, >>> >>> Luca >>> >>> >>> >>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote: >>> >>>> (now with images) >>>> >>>> Dear mailing list members, >>>> >>>> >>>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches. >>>> What could be the reason for that and how could I avoid it? >>>> >>>> Any help or hints are very much appreciated >>>> Roman >>>> >>>> >>>> -- >>>> Dr. Roman Grothausmann >>>> >>>> Tomographie und Digitale Bildverarbeitung >>>> Tomography and Digital Image Analysis >>>> >>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120 >>>> Medizinische Hochschule Hannover >>>> Carl-Neuberg-Str. 1 >>>> D-30625 Hannover >>>> >>>> Tel. +49 511 532-9574 >>>> >>>> >>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------ >>>> 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_feb_______________________________________________ >>>> vmtk-users mailing list >>>> vmt...@li... >>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> -- >> Dr. Roman Grothausmann >> >> Tomographie und Digitale Bildverarbeitung >> Tomography and Digital Image Analysis >> >> Institut für Funktionelle und Angewandte Anatomie, OE 4120 >> Medizinische Hochschule Hannover >> Carl-Neuberg-Str. 1 >> D-30625 Hannover >> >> Tel. +49 511 532-9574 > > ------------------------------------------------------------------------------ > 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_feb > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
