vmtklevelsetsegmentation and vmtkmarchingcubes

[Jesse Ross-Jones]

Dear VMTKrs,

I am trying to write a C++ program to segment and create a mesh object using vmtk. I am using the following as reference:

vmtklevelsetsegmentation -ifile image_volume_voi.vti --pipe vmtkmarchingcubes -i @.o -ofile model.vtp 

Right now I would like simply to use the thresholding initialization type, however I have trouble following the vmtklevelsetsegmentation python script 

My attempt to recreate it is pasted here: http://pastebin.com/rMdsCpgv. Right now I am getting this error: Input port 0 of algorithm vtkvmtkThresholdSegmentationLevelSetImageFilter(08416068) has 0 connections but is not optional.

I know i somehow need to provide an initialization image and I guess this is the origin of the error..

Could someone please help me understand a little better how to use vtkvmtkThresholdSegmentationLevelSetImageFilter.h?

Many many thanks
Jesse

[Luca Antiga]

Hi Jesse,

 I suggest you take a look at this:

https://github.com/Kitware/ITK/blob/master/Examples/Segmentation/ThresholdSegmentationLevelSetImageFilter.cxx

and this

http://www.itk.org/Doxygen/html/classitk_1_1ThresholdSegmentationLevelSetImageFilter.html

since the vmtk class is a wrapper around that ITK class.

Basically the threshold segementation level set image filter is a level set evolution filter that starts from some implicit surface (an image negative inside and positive outside the shape, or the other way around, it's just a convention, whose zero isosurface is the surface you're evolving) and inflates or deflates until it falls within an intensity range given by the lower and upper thresholds. The portion of the surface located in regions of the image that are greater than the upper threshold will deflate, while the portion located in regions lower than the lower threshold will inflate.

The initialization is provided through the call to SetInput and the initial isovalue used to define the initial level set is the one specified in SetIsoSurfaceValue (0.0 in your case, so just make sure your image crosses zero somewhere).

You have SetInput in your code, so you're doing it correctly. Try to call connector->Update() somewhere, e.g. before you set its output as input to the threshold level set filter - it might be a pipeline issue.

Best,

Luca

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[Jesse Ross-Jones]

Hi Luca,
Many thanks for the example and explanation.

I have used that example to generate the attached source code and to generate levelsetTest.vti but when I compare this to the output generated by vmtk(levelsetTestVMTK.vti) it is slightly different but I dont know the cause(could it be from how the image is initialized?). Also when I try to use this file to generate a surface using marching cubes (vmtkmarchingcubes -ifile C:/temp/VMTK_testing/levelsetTest.vti -ofile C:/temp/VMTK_testing/model.vtp )  there is no result (empty polydata). Is there a problem with the parameters I am using perhaps, or the initialization of the image? In this case to initialize I am using a distance map generated by the Danielsson filter.

Many thanks,
Jesse

[Luca Antiga]

Hi Jesse,

 I got around to looking at the data only today.

So, your output image is essentially binary, all voxels are either 0 or 255. This is because you are using

thresholdSegmentation -> thresholdFilter -> writer

The thresholdFilter takes the output from the level set segmentation and binarizes it, which I don't think is what you want if you want to make it look similar to vmtk. 

vmtk outputs a level set, which is an image that has < 0 values inside and > 0 values outside the surface, typically floating point, so that interpolating the 0-isosurface you can get a smooth surface (otherwise you'd see it minecraft-like, as in your output).

Just try to get rid of the thresholdFilter and connect the segmentation filter directly to the writer. Also, use a larger number of iterations, 1 will not do much.

Hope this helps.

Luca