[Insight-users] level set pipeline

[ilker hacıhaliloğlu]

hi Luis

Thanks a alot for the detailed explanation. Well i am working since the
beginning of october with ITK and Level set segmentation.  But i am still
new to ITK an also improving my C++.

First i have worked with the examples given in the software guide I also
used insight applications to tune the pramaters for my data individualy then
last noght i connected this pipeline togehter with this tuned parameters and
it worked really well i can say the the best one till know for my
application which is bone segmentation in MRI.

But i actually want to confirm if i can use a pipeline like this . It made
sense to me and i am using only one seed point and still getting very good
segmentation results.  Thanks a lot Luis for your help right now i will
check the part of the code

Cheers
ilker


On 12/19/05, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
>
> Hi Ilker,
>
> Yes,
> you could try a Level Set Pipeline like this one.
>
> Note however that when you connect the feature image to the
> ThresholdSegmentation Level Set filter what it will do with
> it is to compute its laplacian and multiply it by a factor
> (that you must provide) "EdgeWeight" and will add it to the
> threshold contribution in order to compute a final speed image.
>
> You may want to look at the code in:
>
>
>       Insight/Code/Algorithms
>           itkThresholdSegmentationLevelSetFunction.txx
>
> in lines 31-88 in order to get familiar with the actual operation
> of the filter.
>
>
>
> Take into account that you will have *a lot* of intermediate
> parameters to fine tune on each of the filters involved.
>
> I would strongly suggest to to go step by step, fine tunning
> the parameters of every stage of your pipeline before you add
> the next stage.
>
>
> For example
>
> a) Make sure that the output of the Sigmoid looks almost like
>    a binary image, before you attempt to connect the output to
>    the FastMarching filter.
>
> b) Make sure that you select many seeds close to the medial line
>    of the object to be segmented, and you pass them to the Fast
>    Marching filter.  Make sure that the output of Fast Marching
>    is satisfactory before you attempt to pass it to the Threshold
>    segmentation filter.
>
> c) Fine tune first the threshold values of the Threshold segmentation
>    image filter, and then adjust the value of the EdgeWeight parameter.
>    Make sure that you get a reasonable segmentation before you pass it
>    to the Geodesic active contour filter.
>
> d) Fine tune the three weights of the GeodesicActiveContour filter.
>    If you did a good job in steps (a-c) you will not need a lot of
>    propagation weight, because the level set should already be quite
>    close to the borders of your image. So probably you could focus
>    on the Advection weight and the Curvature weight.
>
>
> Note: You *really* need an intermediate visualizatoin, different from
> just writing images to files. If you don't use an intermediate
> visualization It will take you *a long* time to fine tune all those
> twenty or so parameters in your pipeline.
>
>
> Regards,
>
>
>    Luis
>
>
>
>
>
> --------------------------
> ilker hacıhaliloğlu wrote:
> > hi all
> >
> > i am using the level segmentation methods i am just wondering if i can
> > construct a pipeline like this one ??
> >
> >
> >
> > smoothing->SetInput( reader->GetOutput() );
> >
> > gradientMagnitude->SetInput( smoothing->GetOutput() );
> >
> > sigmoid->SetInput( gradientMagnitude->GetOutput() );
> >
> > fastMarching->SetInput( sigmoid->GetOutput() );
> >
> > thresholdSegmentation->SetInput( fastMarching->GetOutput() );
> >
> > thresholdSegmentation->SetFeatureImage( reader->GetOutput() );
> >
> > geodesicActiveContour->SetInput( thresholdSegmentation->GetOutput() );
> >
> > geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );
> >
> > thresholder->SetInput( geodesicActiveContour->GetOutput() );
> >
> > writer->SetInput( thresholder->GetOutput() );
> >
> >
> >
> > --
> > ------------------------------------------------------------------
> >
> > '.....ich möchte mir eine ader öffnen, die mir die ewige freiheit
> > schaffte....'
> >
> > --------------------------------------------------------------------
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
>
>


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'.....ich möchte mir eine ader öffnen, die mir die ewige freiheit
schaffte....'

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