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

Luis Ibanez luis.ibanez at kitware.com
Fri Dec 3 21:13:43 EST 2004


Hi Neha,

What version of ITK are you using ?

You are probably using the ITK version that used to read the PNG
images inverting the Y access, and therefore the position of the
pixel (30,63) is no longer the center of the tumor.

What are you using to read the Raw image into ITK ?

Did you changes the pixel types in the code in order to match the
input image ?

The parameters of a segmentation method are specific for the input
pixel type, the image modality and the anatomical structures that
you plan to segment.


Please make available the original raw image.


   Thanks


     Luis


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

> Hello Luis,
> Thanks for the reply.  I have chanegd interataions to 100.  But with 
> same png image, I get different result (I have used ctr. as(79,93).  The 
> center that you have specified (30,63) seems to be out of brain area.  
> Also, if i use original raw image, output is blank.  I am not sure what 
> is going wrong.   (I saved original raw image as .png image by making it 
> 8-bits per channel from 16-bit per channel in photoshop , and then sent 
> to you)
> Neha.
> 
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
> 
> 
>     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 borde! r 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 BinaryMedianImage! Filter 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 /* 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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>     ------------------------------------------------------------------------
>      >
> 
> 
> 
>      > ATTACHMENT part 2 image/png name=tumor57Segmented.png
>     *
> 
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