[Insight-users] Re: Brain Tumor + Level Set Filter

[Luis Ibanez]

Hi Neha,

Thanks for posting your image.

The ThresholdSegmentationLevelSet worked fine in this image,

I used the example code in:


      Insight/Examples/Segmentation/
         ThresholdSegmentationLevelSetImageFilter.cxx


Just replaced the maximum number of iteration in line 200.

The current value is 1200 iteration,
you must use here 100 iterations.


Then in the command line use


   ThresholdSegmentationLevelSetImageFilter
             tumor57.png segmented.png  30 63 5  70 207


(in a single command line)

The numbers:   30 63 are respectively the X,Y approximate coordinates
of the tumor center.

The number:  5 is a radius to be used for creating a initial level set
as a circle of radius 5 pixels centered at (30,63).

The numbers: 70 and 207 and the lower and upper thresholds that define
a border for the tumor.



In the future you may find useful to use the interactive application


       InsightApplications/
             ThresholdSegmentationLevelSetFltkGui


That allows you to set all this parameters interactively and see the
evolution of the level set iteration by iteration.

Note that it is *very* important to monitor/supervise the level set
because if you run it for too few iterations the tumor will be under
segmented, an if you run it for too many, the level set will leak and
start invading other brain structures.

Looking at the level set as it is evolving is the best way to figure
out how many iterations are enough for stopping the level set.

By fine tunning the values of the lower/upper thresholds, the curvature
scaling and the number of iterations you will be able to refine the
borders of the segmented region.

You could also post-process the segmented image with a filter such as
the BinaryMedianImageFilter or the new itkVotingBinaryImageFilter.



Please find attached the PNG image with the tumor segmented from your
image.



    Regards,


       Luis



---------------------------------------------------------------------------
neha k wrote:

> Hello Luis,
>  
> Thanks for your reply.  While using this filter, with my Brain tumor 
> Image attached, I am not getting any luck with application, i have tried 
> different parameter values. 
> I am not sure what Level Set filters would be good to delineate tumor in 
> my image attached.  Smoothing did not seem to help for using 
> ThresholdLevelSet and ShapeDetection Level Set.   My original Image is 
> RAW with .mhd header file.
> Any suggestions?  How can I tune pramaters to separate tumor?  What type 
> of preprocessing and other filters might help?
>  
> Thanks,
> Neha
> 
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
> 
> 
>     Hi Neah,
> 
>     Thanks a lot for posting such a detailed message.
> 
> 
>     We attempted to reproduce the result that you reported,
>     but the program worked fine for us.
> 
> 
> 
>     Here are the command line parameters that we used,
>     and the output from the program:
> 
> 
>     A) Command line:
> 
>     ShapeDetectionLevelSetFilter BrainT1Slice.png T1.png
>     81 113 5 1 -0.5 3 0.05 1
> 
>     Output:
> 
>     Max. no. iterations: 800
>     Max. RMS error: 0.02
> 
>     No. elpased iterations: 108
>     RMS change: 0.0199696
> 
> 
> 
>     B) Command line:
> 
>     ShapeDetectionLevelSetFilter BrainProtonDensitySlice.png PD.png
>     81 113 5 1 -0.5 3 0.05 1
> 
>     Output:
> 
>     Max. no. iterations: 800
>     Max. RMS error: 0.02
> 
>     No. elpased iterations: 125
>     RMS change: 0.0189581
> 
> 
>     The output images (T1.png and PD.png) are attached.
> 
> 
> 
> 
>     Did you modified th! e code of this Example
>     in any way before running it ?
> 
> 
> 
>     Please let us know,
> 
> 
>     Thanks
> 
> 
> 
>     Luis
> 
> 
>     --------------------------
>     neha k wrote:
> 
>      > Hello,
>      >
>      > I am trying to check with
>     ITK1.8\Example\ShapeDetectionLevelSetFilter,
>      > and do not get desired output. I tried this compiled example with
>      > following input images and parameters -
>      >
>      > *1. BrainT1Slice.png(input image from \ITK\Examples\Data) - with *
>      >
>      > Seed Point - (81 113) , Distance - 5.0,
>      >
>      > Sigma SigmoidAlpha SigmoidBeta are -- 1 .0 -0.5 3.0
>      >
>      > Curv. Scaling -- 0.05 Propogation Scaling -- 1
>      >
>      > *Output File Name Attached - ShapeDetectionLevelSetFilterOutput4.png*
>      >
>      > *2. BrainProtonDensitySlice.png with Seed Point - (81,114) and
>     rest of
>      > the parameters *have same values as above.
>      >
>      > Problem - Result of SigmoidFilter is Blank Image while output ! of
>      > ShapeDetectionLevelSet Filter for both images is something weird.
>      > (attached files)
>      >
>      > Any input on this appreciated.
>      >
>      > Thanks,
>      >
>      > Neha
>      >
>      >
>      >
> 
> 
>      > ATTACHMENT part 2 image/png name=T1.png
> 
> 
>      > ATTACHMENT part 3 image/png name=PD.png
> 
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