[Insight-users] Extract centerlines from a 3D segmented binary image

[Hui Tang]

Hi all, maybe it is much easier to just use VMTK, there are several papers
describing that tool, including TMI, and it has a very theoretical
definition of centerline from segmented surface. it is easy to use, you do
not need to give any speed functions, you only need to give two seed points
(or they can be  automatically taken as cap centers).  Just download,
compile, then similar to ITK, VTK, write a wrapper, if you do not want to
write a wrapper, there are already quite a lot of python wrappers, just
grap one,play with it.
Anyway I would strongly recommend VMTK.

On Tue, Apr 10, 2012 at 1:13 PM, Sergio Vera <sergio.vera at alma3d.com> wrote:

> Would the ridges of the Distance map  work as  good speed image?
> Other than being close to 1 near the centerline. Perhaps the averagw
> outward flux of the distance map (~= risges of the distance map) ,
> normalized properly top 0-1 would do the trick.
>
>
> On Mon, Apr 9, 2012 at 11:13 PM, Dan Mueller <dan.muel at gmail.com> wrote:
>
>> Hi superZZ,
>>
>> Good to hear the approach is suitable for your needs.
>>
>> Cheers, Dan
>>
>> On 10 April 2012 03:01, jxdw_zlf <jxdw_zlf at yahoo.com.cn> wrote:
>> > Dear Dan,
>> >
>> > Thank you! It works fine now. Really appreciate for your help :)
>> >
>> > Best Regards,
>> >
>> > superZZ
>> >
>> >
>> > ------------------ Original ------------------
>> > From:  "Dan Mueller"<dan.muel at gmail.com>;
>> > Date:  Mon, Apr 9, 2012 08:41 PM
>> > To:  "zlf"<jxdw_zlf at yahoo.com.cn>;
>> > Cc:  "insight-users"<insight-users at itk.org>;
>> > Subject:  Re: [Insight-users] Extract centerlines from a 3D segmented
>> binary
>> > image
>> >
>> > Hi superZZ,
>> >
>> > To reiterate my first email: this method is a little tricky due to the
>> > need for a _good_ speed function. A good speed function has high
>> > values (~1.0) near the centerline and low values (0.0) away from the
>> > centerline.
>> >
>> > A distance map can be used generate such a speed function, but the
>> > output of the distance map is _NOT_ the speed function: the distance
>> > map requires further processing!
>> >
>> > Here are the steps I used to quickly generate a speed function
>> > (commands are in SharpImage syntax, a custom prototyping environment
>> > of mine, but you should be able to work out what is happening):
>> >
>> > SignedMaurerDistance
>> > SmoothingRecursiveGaussian Sigma=1.0
>> > Threshold Lower=-10 Upper=100 OutsideValue=-10
>> > RescaleIntensityToF OutputMinimum=0.0 OutputMaximum=1.0
>> > UnaryPixelMath Operation="Power" Exponent=3
>> >
>> > The results look acceptable to me (see attached).
>> >
>> > HTH
>> >
>> > Cheers, Dan
>> >
>> > On 9 April 2012 16:26, zlf <jxdw_zlf at yahoo.com.cn> wrote:
>> >> Dear Dan,
>> >>
>> >> I process airway.mhd with SignedMaurerDistanceMapImageFilter. Pass
>> >> SignedMaurerDistanceMapImageFilter's result as speed image. The result
>> is
>> >> even worse.
>> >>
>> >>
>> >>
>> http://itk-insight-users.2283740.n2.nabble.com/file/n7449026/centerline_SignedMaurerDistanceMapImageFilter.jpg
>> >>
>> >> Regards,
>> >>
>> >> superZZ
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>
>
>
> --
> Sergio Vera
>
>  Alma IT Systems
>  C/ Vilana, 4B, 4º 1ª
>  08022 Barcelona
>  T. (+34) 932 380 592
>  www.alma3d.com
>
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