Dear all,
From http://hdl.handle.net/1926/576 page 3, paragraph after eq. 11 I understand that itkHessianToObjectnessMeasureImageFilter only can enhance structure of dimension m=0, 1 or n-1. In case n=3, m=2=n-1 (my case) this would be just what I need but my tests yielded identical results for m= 1 or 2 (same md5sum for both outputs:-( ). Based on table 1, p 133 of (A. F. Frangi et. al Multiscale vessel enhancement filtering, 1998) I would expect that to enhance plate-like structures the weighting function would have to be changed in such a way that when the three eigenvalues full fill l1~l2<<l3 (instead of l1<<l2~l3 for vessels), Ra->inf and Rb->0. Accordingly, the weighing function e.g eq. 1 in http://hdl.handle.net/1926/576 enhances structures for which Ra~1 and Rb~0. Using eq. 10 and 11 (http://hdl.handle.net/1926/576) for m=n-1: Ra is not defined and Rb=l2/l3~0. However, I would think that exchanging l1 and l3 and using Rb=l2*l1/l3 in the weighing function would again lead to Ra~1 and Rb~0. I've to check if for some reason my code-modifications caused something different. Many thanks for all Your help and suggestions. Roman On 05/09/12 15:01, Luca Antiga wrote: > Dear Roman and all, the itkHessianToObjectnessMeasureImageFilter in > ITK Review should allow you to select the target object > dimensionality (blob vs line vs plate) by calling SetObjectDimension > (0 vs 1 vs 2, respectively; as a note, the filter with dimensionality > 1 corresponds to Frangi's vesselness). One aspect you should be very > careful about is the scale (or the scale range if you use this filter > through itkMultiScaleHessianBasedMeasureImageFilter) expressed in > physical units. You can get an example of the use of the filter here > http://hdl.handle.net/1926/576 Hope this helps > > Luca > > > On Sep 5, 2012, at 2:41 PM, Ho Cheung wrote: > >> 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.ro...@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 _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://www.itk.org/mailman/listinfo/insight-users >> > -- 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 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. 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