[Insight-users] label object manipulation

[Badri Roysam]

In the interim, it should be possible to resample images to make them quasi-isotropic and
user Dirk's filters.


Badri Roysam
Professor, Department of Electrical, Computer and Systems Engineering
Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC)
Co-Director, Rensselaer Center for Open Source Software
Rensselaer Polytechnic Institute
110 8th Street, Troy, New York 12180-3590, USA.
Office(JEC 7010): 518-276-8067, Assistant: 518-276-8525, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715
Email: roysam at ecse.rpi.edu, Web: http://www.ecse.rpi.edu/~roysam



----- Original Message -----
From: Padfield, Dirk R (GE, Research) [mailto:padfield at research.ge.com]
To: Gaëtan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr], lynx.abraxas at freenet.de
Cc: insight-users at itk.org
Subject: Re: [Insight-users] label object manipulation


> Hello Gaëtan,
> 
> Thanks a lot for your message.  As you mentioned, the
> itkLabelGeometryImageFilter does not yet take pixel spacing into account,
> and I need to find time to make this extension.  This extension should,
> however, be fairly straightforward.  For the problem of including the voxel
> thickness in the moment calculation, I believe the derivation of Equation 20
> in the itkLabelGeometryImageFilter documentation
> (http://insight-journal.com/download/viewpdf/301/4/download) should be
> useful since it is derived by analytically calculating the moment of a
> pixel.  It should be easy to generalize this derivation to take into account
> pixel spacing.
> 
> I hope this helps,
> Dirk.
> 
>  
> 
> -----Original Message-----
> From: Gaëtan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr] 
> Sent: Tuesday, June 30, 2009 5:00 AM
> To: lynx.abraxas at freenet.de; Padfield, Dirk R (GE, Research)
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] label object manipulation
> 
> 
> Le 29 juin 09 à 23:31, lynx.abraxas at freenet.de a écrit :
> 
> > Dear Gaëtan Lehmann,
> >
> >
> > Thanks  a  lot  for You quick answer. With Your hints it was easy to 
> > extend my little program to suit my needs further.
> > I'm wondering though if the article is the best documentation to work 
> > with.  I
> > couldn't   find   the   Perimeter   attribute   only   
> > EquivalentPerimeter  and
> > EquivalentEllipsoidPerimeter. The connectivity is also only mentioned  
> > in  the examples.  Is there another documentation where these are 
> > explained and that I should read before asking here?
> >
> 
> No, there is no other document, but you can look at the source! All the
> attributes are listed in
> 
>   
> http://voxel.jouy.inra.fr/darcs/contrib-itk/binaryAttributeMorphology/itkShapeLabelObject.h
>   
> http://voxel.jouy.inra.fr/darcs/contrib-itk/binaryAttributeMorphology/itkStatisticsLabelObject.h
> 
> And you're right, I forgot to put the perimeter in the attribute list.  
> I'll try to fix that in a next revision.
> 
> > In the footnote it says there'll be more about perimeter estimation in 
> > another article. Is that published already?
> >
> 
> No, not yet.
> 
> > I  noticed  that GetEquivalentEllipsoidSize yields nan/inf if the 
> > bounding box is only 1 pixel wide. When I used the image moments of 
> > Avizo to calculate  the axes lengths a bounding box width of 1 pixel 
> > wasn't a problem. I'm not sure if
> > this result from Avizo is good but with my current understanding a   
> > full  axis
> > length of 1 (or 0.5 for a semi axis) would be sensible, wouldn't it?
> 
> I have this problem also, and it's quite annoying. It's caused by an
> approximation in the moment computations: the voxel thickness is not used.
> The formulae I used are very common, and I didn't find an easy way to
> include it. In http://insight-journal.com/browse/publication/301 , this
> information is used, but unfortunately, the spacing is not.
> Also, I don't think that putting 1 (or 1/2) axis if the size is 0 on this
> axis would be nice, because it would make the result quite different of the
> case where there the size is very thin but not zero.  
> Something like
> 
>     0000000000000000000000000000
> 
> and
> 
>     0000000000000000000000000000
>            0
> 
> 
> > If  it's not possible to calculate that, would it be possible to get 
> > an output letting the filter assume only 2D for these objects?
> 
> 
> I would prefer getting a non-approximated formulae for the moment
> computation which take care of the spacing. I'm quite sure it's not that
> complicated, but, well, that's not my field of competences.
> 
> If someone has some documentation, or has the needed knowledge on that
> point, I would really appreciate some help!
> 
> Gaëtan
> 
> 
> 
> 
> --
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction INRA de Jouy-en-Josas
> (France)
> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr  http://www.itk.org http://www.mandriva.org 
> http://www.bepo.fr
> 
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