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

Wed Sep 5 12:03:04 EDT 2012

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.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 _____________________________________
>>> 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