Well...I'm not using vmtkbranchextractor. My branches and vessel are defined separately, and I merge them in a pre-vmtk process. I have centerlines a priori, but it is not a unified centerline tree. (I have until now been using source and target points. This works well in most vessels, but heavily branched ones frequently drop a branch, often the largest one, during the run of vmtkcenterlines, so after reading this thread, I concluded I wasn't alone, and set about trying to reengineer it.)
I just tried running it with groupID==centerlineID for all centerlines, and tractID = uniformly 1, and blanking = uniformly 0. The result was an unruly knot that suggested that it didn't know what to connect to what. I suspect, after digging through the vtkVmtk source code and looking at this http://www.vmtk.org/Tutorials/BranchSplitting/ example, I need to actually annotate the bifurcation regions by setting group and tract id, and blanking, correctly. If I understand this correctly, I can create a bifurcation region by identifying where the branch departs the vessel, and appending 1 location on the vessel centerline to the branch centerline at the proximal-most location. And then, groupID increments at and after each bifurcation region, and blanking is set to 1 in each bifurcation region. I'm less clear on tract ID. Is it always either 1 or 2, depending whether before or after the bifurcation point? Or does it get set to a unique value for each chunk vis a vis group id? I won't be able to get to it until this evening, but I believe that's the next logical step. -rd On 03/07/2013 10:35 AM, Luca Antiga wrote: > Hi Richard, > just pipe vmtkcenterlinemerge after vmtkbranchextractor and use -ofile to > write the file out, that's the quickest. > What is your exact issue? > > Roman: I haven't got an answer for you yet - I've been taking care of the > quick messages but yours requires a free slot of time. Thanks for your > patience. > > Luca > > On 06/mar/2013, at 18:31, Richard Downe <richard-do...@uiowa.edu> wrote: > >> 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 >>>>>> vmtk-users@lists.sourceforge.net >>>>>> 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 >>> vmtk-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users ------------------------------------------------------------------------------ Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev _______________________________________________ vmtk-users mailing list vmtk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users
