Hi Roman, you have an interesting case here. As I wrote in another message a couple of minutes ago, vmtkcenterlines can't handle loops, but this is not the case here.
What happens is that the internal delaunay diagram is not extracted correctly. A few elongated tetrahedra in correspondence of some of the outlets that are considered "internal" (although they are not) and this creates artifactual shortest paths from the inlet to some of the outlets that run through those external tetrahedra (the paths you showed in gray). These paths are chosen as optimal, so the corresponding true inner paths are lost. 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 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 ... 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 > vmtk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/vmtk-users ------------------------------------------------------------------------------ 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 vmtk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users
