Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

[Luca A. <luc...@or...>]

Hi Richard,
 indeed there is a way. The initialization phase in vmtklevelsetsegmentation is performed by vmtkimageinitialization,
which accepts parameters at the command line and whose output can be piped to vmtklevelsetsegmentation (in which
case the latter will use the initialized level sets generated by the former). vmtklevelsetsegmentation can also run
non-interactively by specifying iterations and evolution parameters at the command line. Here's a sample pipe:

vmtkimageinitialization -ifile your_image_file.mha -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1 -propagation 0.0 -ofile level_set_file.mha

One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e. voxel indices), not physical coordinates.

Hope this helps,


Luca


On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:

> Hello,
> 
> I'm interested in calling vmtkLevelSetSegmentation from a script. I want to run colliding fronts with arbitrary thresholds and start/end position vectors for the initial segmentation, and then run the level set segmentation with arbitrary parameters.
> 
> Unfortunately, there doesn't seem to be any way to specify these parameters from the command line. What might be the easiest way to accomplish this?
> 
> Thanks,
> Richard
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