[ITK] [ITK-users] [Insight-users] enhancing plate like structures (by modifying itkHessianSmoothed3DToVesselnessMeasureImageFilter)
Dr. Roman Grothausmann
grothausmann.roman at mh-hannover.de
Fri Aug 15 08:44:40 EDT 2014
Dear Michel, dear Luca,
Coming back to Hessian-based measures of Yours, which I've tried out two years ago:
Is my understanding correct that the response function V of [Descôteaux et.
al.MICCAI 2006] and [Luca ITK-Journal 2007] differ for N=3 and M=2?
i.e. for N=3, M=2:
Rblob = vnl_math_abs( l3 + l3 - l2 - l1 ) / l3 in itkDescoteauxSheetnessImageFilter
corresponding to Ra (NOT Rb) in itkHessianToObjectnessMeasureImageFilter, which
is undefined for N=3, M=2.
Rsheet = l2 / l3 in itkDescoteauxSheetnessImageFilter
corresponds to Rb in itkHessianToObjectnessMeasureImageFilter, both equal for
N=3, M=2.
When has each definition its optimal use?
Additionally, In Descôteaux2006 a zero level-set segmentation approach is
described based on a vector field constructed from initial ellipsoids positioned
at high sheetness measures.
Are there ITK-Filters to achieve that same approach or something similar? Which
would I need?
Many thanks again for Your replies and help.
Roman
On 05/09/12 17:10, Audette, Michel A. wrote:
> Do a google on sheetness. Maxime Descôteaux and I had modified this type of
> operator a few years back to improve the detection of curviplanar bones (MICCAI
> paper, republished in J. Computer Assisted Surgery), which was a tweak of his
> and Frangi's work on vesselness operators.
>
> Michel
>
> Michel Audette, Ph.D.
> Assistant Professor,
> Department of Modeling, Simulation and Visualization Engineering,
> Old Dominion University,
> Norfolk, VA.
> ________________________________________
> From: insight-users-bounces at itk.org [insight-users-bounces at itk.org] on behalf of
> Ho Cheung [hocheung20 at gmail.com]
> Sent: Wednesday, September 05, 2012 8:41 AM
> To: Dr. Roman Grothausmann
> Cc: insight-users at itk.org; vmtk-users at lists.sourceforge.net; Luca Antiga
> Subject: Re: [Insight-users] enhancing plate like structures (by modifying
> itkHessianSmoothed3DToVesselnessMeasureImageFilter)
>
> Hi Dr. Grothausmann,
>
> The measure in ITK appears to be based on Sato
> (http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/yoshi/node3.html#SECTION00021000000000000000)
> and I don't see an easy way to modify it so that it detects plate like
> structures instead of line like structures.
>
> If speed is not a major concern for you, may I suggest you implement a similar
> measure? Frangi's original vesselness enhancement formula
> (http://www.dtic.upf.edu/~afrangi/articles/miccai1998.pdf) can be easily
> modified for what you need and is based on Eigenvalues like Sato.
>
> According to equations 10, 11, 12, 13 in Frangi's paper and my interpretation of
> what the measures do, what you need is high Ra, Rb, and S values, so the formula
> becomes:
>
> V = [1 - exp(-Ra^2/2a^2)][1 - exp(-Rb^2/2b^2)][1 - exp(-S^2/2c62)]
>
> Hope, this helps,
>
> Ho Cheung
> Research Assistant
> Bio-Image Analytics Laboratory - University of Houston
> (832) 215-6347
>
>
>
> On Sep 5, 2012, at 3:36 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>
> > Dear mailing list members, dear Luca,
> >
> >
> > Recently I was trying to enhance vascular structures from airways with the
> vessel enhancement filters from ITK (objectness and vessel enhancement). The
> problem is that these vessels are not filled in the tomograms our imaging
> technique yields. Only the airway walls are imaged, which corresponds to an
> uneven 2D surface. Since it is only a 3D not an ND problem, I tried to modify
> itkHessianSmoothed3DToVesselnessMeasureImageFilter to enhance not vessels (1D)
> structures but plates/walls. Therefore I exchanged lambda 1 and 3 in the
> weighting function. Sadly, I could not get the filter to enhance the airway walls.
> > Have I missed anything or would enhancing plateness this way only work for
> not-curved planes?
> >
> >
> > Here the important part of the diff of my changes:
> >
> > diff -au
> itk/IJ-Vessel_Enhancement_Diffusion.1/itkHessianSmoothed3DToVesselnessMeasureImageFilter.txx
> itk/plateness3D_01/itkHessianSmoothed3DToPlatenessMeasureImageFilter.txx
> >
> >
> >
> > + ////swap Lambda1 and Lambda3 to enhance "plateness"
> > + double swap_tmp= Lambda1;
> > + Lambda3= Lambda1;
> > + Lambda1= swap_tmp;
> > + ///swapping done
> > +
> > double Lambda1Abs = vnl_math_abs( Lambda1 );
> > double Lambda2Abs = vnl_math_abs( Lambda2 );
> > double Lambda3Abs = vnl_math_abs( Lambda3 );
> > @@ -162,14 +168,13 @@
> > double vesMeasure_3 =
> > ( 1 - vcl_exp( -1.0 * (( vnl_math_sqr( S )) / ( 2.0 * ( GammaSqr)))));
> >
> > - double vesMeasure_4 =
> > - vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C )) /
> > - ( Lambda2Abs * (Lambda3Sqr)));
> > + double vesMeasure_4 = 1; ////plateness for now not smoothed
> > + //double vesMeasure_4 = vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C ))
> / ( Lambda2Abs * (Lambda3Sqr))); ////check if this makes sense for plateness
> >
> >
> > Many thanks for any help or hints.
> > Roman
> >
> > --
> > Dr. Roman Grothausmann
> >
> > Tomographie und Digitale Bildverarbeitung
> > Tomography and Digital Image Analysis
> >
> > Institut für Funktionelle und Angewandte Anatomie, OE 4120
> > Medizinische Hochschule Hannover
> > Carl-Neuberg-Str. 1
> > 30625 Hannover
> >
> > Tel. +49 511 532-9574
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--
Dr. Roman Grothausmann
Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis
Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover
Tel. +49 511 532-9574
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