[Insight-users] GeodesicActiveContourLevelSetImageFilter output- help needed

[Luca Antiga]

Hi Gita,
  the -4 +4 values depend on the way SparseFieldLevelSetImageFilter is
implemented, segmentation parameters won't have any effect on that.

Level set segmentation produce a surface in output, which is the surface
located at the zero-level of your output volume. Note that the zero  
level
may not be defined exactly at a voxel, but may be located on an edge
between two voxels, e.g. in 1D, you may have
-0.5    0.5
+-----+
with your zero level located in the middle of the edge. Similarly for  
nD.
In fact, the level set volume represents an approximate distance  
function
from the zero level surface. To save in computational resources, such  
function
is built for 4 layers around the zero level set (hence the -4 +4).
Those intermediate values you mention (-1 +1, ...) are the values of  
the distance
function whose zero level describes the surface.
The bottomline is, the (interpolated) zero level set surface is what  
you're interested
in, don't worry about the other values.

There's one point I don't understand: how is it that playing with  
sigma makes -1 +1
disappear? For some reason I can't open your images: can you post  
them in another
format?

Regards

Luca



On Jul 3, 2008, at 2:00 AM, Gita wrote:

>
> Hallo All,
>
> I am trying to use a GeodesicActiveContourLevelSetImageFilter to fine
> tune my segmented image.
> The segmented image is used as the initial level set and the raw scan
> (after processed by Smoothing, Gradient Magnitude and Sigmoid filters)
> is used as the feature image. A sigma value of 0.5 is used for  
> Smoothing
> filter. The values of alpha and beta (for Sigmoid filter) are -12  
> and 49
> (as K1=85, k2=13 for the image at the output of GradientMagnitude
> filter). The value of propagationScaling is 1.
>
> The input images have been re-sampled to produce isotropic voxels and
> the output pixel type has been set as float.
>
> A portion of my code:
>
> typedef  itk::GeodesicActiveContourLevelSetImageFilter<FType, FType >
> GeodesicActiveContourFilterType;
>   GeodesicActiveContourFilterType::Pointer geodesicActiveContour =
> GeodesicActiveContourFilterType::New();
>   geodesicActiveContour->SetPropagationScaling( propagationScaling );
>   geodesicActiveContour->SetCurvatureScaling( 1.0 );
>   geodesicActiveContour->SetAdvectionScaling( 1.0 );
>   geodesicActiveContour->SetMaximumRMSError( 0.02 );
>   geodesicActiveContour->SetNumberOfIterations(800 );
>   geodesicActiveContour->SetInput(inputSeg);//initial level set
>   geodesicActiveContour->SetFeatureImage(sigmoid->GetOutput()
> );//feature image
>   geodesicActiveContour->Update();
>   writeIm<FType> (geodesicActiveContour->GetOutput(), "geo.nii.gz");
>
> Please find attached files for segmented and output images.
>
> Q1: The output image geo.nii.gz i.e output of
> GeodesicActiveContourLevelSetImageFilter) has a value of 4 in the
> innermost region, then 1, then 0, then 1 and -4. Please see the  
> attached
> file. The contour having a value of 0 is rather closer to my initial
> segmentation. The one with -4 makes the vessels much fatter. I  
> thought I
> should get a 0-value corresponding to boundary, +ve inside & -ve
> outside. I do not understand why I get 1-0-1 layers. Although while
> playing with the value of sigma I noticed significant changes in the
> output. For ex. with sigma=3, 1-0-1 almost disappears from boundary as
> seen in the attached image. However, for some slices I still get  
> values
> other than 4 in the inside region which leads to funny results. I  
> tried
> to change propagation, curvature and advection values as well as the
> number of iterations. None of them had any effect on output except  
> sigma.
>
> How can I choose the parameters that will produce good segmentation.
>
> Q2: Also, what determines the value of 4/-4? Is it determined by the
> value of alpha and beta? I tried to use a different ratio but the  
> output
> is still the same.
>
> Any help would be greatly appreciated.
> Kind regards,
> Gita Das
> http://www.nabble.com/file/p18249367/geo.nii.gz geo.nii.gz
> http://www.nabble.com/file/p18249367/bourkeleft2_carotid_seg.nii.gz
> bourkeleft2_carotid_seg.nii.gz
>
>
> -- 
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> GeodesicActiveContourLevelSetImageFilter-output--help-needed- 
> tp18249367p18249367.html
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>
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