[Insight-users] enhancing plate like structures (by modifying itkHessianSmoothed3DToVesselnessMeasureImageFilter)

Wed Sep 5 12:08:01 EDT 2012

Dear Michel, dear Matt,

Thanks for Your hints. I'll try Your implementations. So far I had 
limited my search to plateness and had not considered the word sheetness.

Many Thanks
Roman

On 05/09/12 17:47, Matt McCormick wrote:
> Hi Roman,
>
> We (Andinet Enquobarhrie) are working on a SheetnessImageFilter in TubeTK:
>
>    http://tubetk.org/
>    http://tubetk.org/gitweb?p=TubeTK.git;a=blob;f=Base/Filtering/itkSheetnessMeasureImageFilter.h;h=38b501eb9f5bc77e0b1d2b88c2b6c8ebc9fdc036;hb=635b5521a82dd3e333fa6febb01a5eabc1b3c7ba
>
> Hope this helps,
> Matt
>
> On Wed, Sep 5, 2012 at 11:10 AM, Audette, Michel A.<maudette at odu.edu>  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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>>
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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
30625 Hannover

Tel. +49 511 532-9574