[ITK] [ITK-users] speed function for itkSpeedToPathFilter

[Prashanth]

Matt and Dan - Thank you so much for getting back to me.

Dan - If I understood your email correctly then a binary image (with 1
inside the vessels and 0 outside) should work as a speed function. And if
that is the case then a binary mask did not work for me. I get no points in
the output of SpeedToPath filter if I use a binary mask. I'm looking into
White top hat filtering and vesselness currently. Like you pointed out (and
as mentioned in your thesis), vesselness is slower but so far it seems to
be working better than white top hat.

Matt - I will look into TubeTk as well and post an update to the mailing
list.

Thanks again
Prashanth

On Tue, Aug 25, 2015 at 10:52 AM Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Prashanth,
>
> Classes within TubeTK [1] specialize in creating input images that
> would work well as an input to the itk::SpeedToPathFilter.
>
> Hope this helps,
> Matt
>
> [1] https://github.com/KitwareMedical/TubeTK
>
> On Sun, Aug 23, 2015 at 5:49 AM, Dan Mueller <dan.muel at gmail.com> wrote:
> > Hi Prashanth,
> >
> > Essentially you want your speed function to be white (1.0) in the
> > vessels and black (0.0) outside of the vessels — any way you can
> > achieve this is fine. The method you have outline is very general, and
> > the issue is step (1) i.e. finding an approximate centreline. Some
> > have suggested achieving this by applying multiscale Hessian line
> > filtering (aka vessel enhancement filtering) such as Sato/Frangi
> > method — while this can achieve good results, personally I find this
> > method very slow. In my own work, I have found morphological top-hat
> > by opening (aka white top-hat or WTH) produces good results at a
> > fraction of the computation expense, especially using the box
> > structuring element with acceleration (e.g. see [1]).
> >
> > Good luck.
> >
> > Cheers, Dan
> >
> > [1] “Direct volume illustration for cardiac applications,” chapter 4,
> > page 83–109, http://eprints.qut.edu.au/17028/1/Daniel_Mueller_Thesis.pdf
> >
> > On 22 August 2015 at 06:52, Prashanth <prashanth.dumpuri at gmail.com>
> wrote:
> >> All,
> >>
> >> I'm working on finding the shortest path between two points in a vessel
> >> tree. itkSpeedToPathFilter seems to be working well for me as long as I
> >> select the right speed function. Digging through Insight Journal, I
> found a
> >> link to Deschamp's Ph.D. thesis
> >> (
> https://tel.archives-ouvertes.fr/file/index/docid/45537/filename/index.html
> )
> >> which outlines one method to select a speed function:
> >>
> >> 1. Approximate centerline based on the input image
> >> 2. Segmentation using the approximate centerline
> >> 3. Use the segmented image and approximate centerline to create an image
> >> with signed distances to the approximate centerline
> >> 4. Use the above image as the  input speed function for
> itkSpeedToPathFilter
> >>
> >> The above steps seem to work (I say 'seem to work' because I tested it
> just
> >> three 2D images so far), but are there other methods to select the speed
> >> function? My input images are contrast enhanced CT images and the
> vessels
> >> are easy to identify and segment. Any help on how to select the correct
> >> speed function will be appreciated.
> >>
> >> Thanks
> >> Prashanth
> >>
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