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
>> >
>> >
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>>
>>
>
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