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
> >
> >
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