Dear Luca,
Thanks for looking into this. It seems that the reason I got exactly the same results for dim 1 or 2 was related to an older ITK installation (3.16) on a machine that has a lot of RAM. When I tried it on a PC with itk 3.20.1 with a smaller dataset I got different results for dim 1 or 2 which look as expected. Now I have to play around with the parameters a bit. I'll use vmtkobjectenhancement for this. Again, many thanks for looking into this and Your contribution Roman On 06/09/12 12:50, Luca Antiga wrote: > Dear Roman, > I ran the itkHessianToObjectnessMeasureImageFilter with m=0, 1, 2 > and the following parameters: > sigma 1.0 > alpha 0.5 > beta 0.5 > gamma 5.0 > on a test image. It looks to me that the filter behaves as expected. > > You can find the input image and the corresponding results here: > https://dl.dropbox.com/u/6585423/object_enhancement.zip > > To get to this quicker I used the version in vmtk, which is analogous > to that in Code/Review. The vmtk script is > > vmtkobjectenhancement -ifile foo.mha -ofile foo_0.mha -dimension 0 > vmtkobjectenhancement -ifile foo.mha -ofile foo_1.mha -dimension 1 > vmtkobjectenhancement -ifile foo.mha -ofile foo_2.mha -dimension 2 > > Hope this helps > > > Luca > > > > On Sep 5, 2012, at 6:03 PM, Dr. Roman Grothausmann wrote: > >> 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 > -- 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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