Hi Luca, Thanks for your help so far. I was looking at your journal article that was published in Stroke back in 2005, and I was wondering how you were able to visualize the inscribed spheres used to generate the centerline. Is there a function in vmtk that is able to do this? Please see photo below.
Thanks, Joe [image: image.png] On Thu, Jan 19, 2012 at 5:09 AM, Luca Antiga <luca.ant...@orobix.com> wrote: > Hello Joe, > I see you already solved the problem. Probably the data you wanted to > access was attached to cells, rather than to points. > Just so you know, the pointdata format (.dat) by default outputs data > attached to points, but you can switch to cell-attached > data using the -celldata 1 flag on the writer > > vmtkcenterlinesections > -ifile neurosurgery/RICA_Pt001_1010rev.vtp > -centerlinesfile neurosurgery/RICA_Pt001_centerline_smooth.vtp > --pipe vmtksurfacewriter -i @.ocenterlines -celldata 1 > -ofile neurosurgery/sectiondata.dat > > Best regards > > > Luca > > > On Jan 18, 2012, at 6:29 PM, Joe Santore wrote: > > Luca, > I just realized that I was able to access the data by changing the output > file from a .dat file to a .vtp file. I'm not sure why this is the case, > but it works. > > Joe > > On Tue, Jan 17, 2012 at 6:39 PM, Joe Santore <joesant...@gmail.com> wrote: > >> Hi Luca, >> Branchclipper fixed the error, but I'm only getting X,Y, and Z >> coordinates in the output file; there is no other data. I was able to run >> centerlinesections without a problem: >> vmtkcenterlinesections >> -ifile neurosurgery/RICA_Pt001_1010rev.vtp >> -centerlinesfile neurosurgery/RICA_Pt001_centerline_smooth.vtp >> -ocenterlinesfile neurosurgery/sectiondata.dat >> >> Thanks for the quick response, >> Joe >> >> >> On Fri, Jan 13, 2012 at 8:43 AM, Luca Antiga <luca.ant...@orobix.com>wrote: >> >>> Hi Joe, >>> I can't test it right away, but it looks to me like you're missing a >>> step in which you clip the surface into branches according to the extracted >>> centerline branches: >>> >>> vmtksurfacereader >>> -ifile neurosurgery/RICA_Pt001_1010rev.vtp >>> --pipe vmtkbranchextractor >>> -ifile neurosurgery/RICA_Pt001_centerline_smooth.vtp >>> -radiusarray@ MaximumInscribedSphereRadius >>> --pipe vmtkbranchclipper >>> --pipe vmtkbifurcationsections >>> -distancespheres 5 >>> -ofile neurosurgery/bifurcationsections.dat >>> --pipe vmtkbranchsections >>> -ofile neurosurgery/branchsections.dat >>> >>> Note that using >>> >>> -radiusarray@ MaximumInscribedSphereRadius >>> >>> I'm forcing radiusarray to be pushed through the pipe, so you don't need >>> to specify it for the subsequent scripts. >>> >>> Hope I nailed it. >>> >>> Best regards >>> >>> >>> Luca >>> >>> >>> On Jan 12, 2012, at 7:42 PM, Joe Santore wrote: >>> >>> > Hi, >>> > I'm getting an error that says "GroupIdsArray with name specified does >>> not exist." It occurs for both of these functions, and I have them piped >>> so that they directly receive the data from branchextractor: >>> > vmtksurfacereader >>> > -ifile neurosurgery/RICA_Pt001_1010rev.vtp >>> > --pipe vmtkbranchextractor >>> > -ifile neurosurgery/RICA_Pt001_centerline_smooth.vtp >>> > -radiusarray MaximumInscribedSphereRadius >>> > --pipe vmtkbifurcationsections >>> > -distancespheres 5 >>> > -radiusarray MaximumInscribedSphereRadius >>> > -groupidsarray GroupIds >>> > -ofile neurosurgery/bifurcationsections.dat >>> > --pipe vmtkbranchsections >>> > -radiusarray MaximumInscribedSphereRadius >>> > -groupidsarray GroupIds >>> > -ofile neurosurgery/branchsections.dat >>> > >>> > I've been trying to get this to work for some time, but everything >>> I've tried has failed. I know that branchextractor is passing GroupIds >>> because branchgeometry and bifurcationvectors work well when I pipe them. >>> > >>> > I would appreciate any advice you can give me, >>> > Joe >>> > >>> > >>> ------------------------------------------------------------------------------ >>> > RSA(R) Conference 2012 >>> > Mar 27 - Feb 2 >>> > Save $400 by Jan. 27 >>> > Register now! >>> > >>> http://p.sf.net/sfu/rsa-sfdev2dev2_______________________________________________ >>> > vmtk-users mailing list >>> > vmtk-users@lists.sourceforge.net >>> > https://lists.sourceforge.net/lists/listinfo/vmtk-users >>> >>> >> > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > > http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ > > vmtk-users mailing list > vmtk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/vmtk-users > > >
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