[Insight-users] Watershed Behavior

Thu Feb 8 19:58:37 EST 2007

I see what you mean. That is a mystery.

Can you package the code and input image too. This certainly suggests
a bug that we should sort out.

On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> Sorry. I can't seem to be able to save anything correctly. So I've attached
> my ANALYZE output volume in 32 bit int format which can be opened with
> MRIcro.
>
>     http://www.ece.ubc.ca/~alberth/watershed_checker_label.img.gz
>     http://www.ece.ubc.ca/~alberth/watershed_checker_label.hdr
>
> Thanks
> Albert
>
> ----- Original Message -----
> From: "Richard Beare" <richard.beare at gmail.com>
> To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> Cc: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>; <insight-users at itk.org>
> Sent: Thursday, February 08, 2007 4:33 PM
> Subject: Re: [Insight-users] Watershed Behavior
>
> The png I get from the website is 8 bit - I can't see the problem.
>
> Can you try unsigned short tif or your current pixel type as nii.
>
> Thanks
>
> On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > Thanks for the fast reply Richard.
> >
> > I quickly remove the relabel filter and save the output of watershed as
> > unsigned int. As you can see with the grayscale image here:
> >     http://www.ece.ubc.ca/~alberth/watershed_morph2.png
> > The outputs are labeled as:
> >     001 002 003 004 005 006 007 ... 018 <---------- topmost
> >     325 326 327 328 329 330 331 ... 342
> >             ..........
> >     019 020 021 022 023 024 025 ... 036
> >     001 002 003 004 005 006 007 ... 018 <---------- bottommost
> > Where the topmost and bottommost rows are labeled as the same numbers or
> > wrap around as I called it.
> >
> > Albert
> >
> > ----- Original Message -----
> > From: "Richard Beare" <richard.beare at gmail.com>
> > To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> > Cc: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>;
> > <insight-users at itk.org>
> > Sent: Thursday, February 08, 2007 2:58 PM
> > Subject: Re: [Insight-users] Watershed Behavior
> >
> > Hi,
> > I'm having difficulty determining what you mean by wrap around - from
> > the example it looks as though it could be wrap around of the
> > colormap, rather than the watershed.
> >
> > Try saving the output of the watershed filter, rather than the
> > relabeller/coloring step and probe the values. For example, save as
> > unsigned short tif and use the ImageView or some other tool to check
> > the values. There shouldn't be any wrap around, but you never know.
> >
> > On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > > Thanks Richard and Gaetan
> > >
> > > The new filter works very well on the edges for my application. However,
> > > when I relabel my image after the morphological watershed, I get a wrap
> > > around on the very top and bottom grids (even though they are
> > > alternating
> > > intensity blocks). Is that a known behavior?
> > >
> > >         http://www.ece.ubc.ca/~alberth/watershed_morph.png
> > >
> > > The left and right image edge labels are ok with no wrap around.
> > > Checking
> > > the gradient magnitude image, all image edges have 0 gradient (top,
> > > bottom,
> > > left, right).
> > >
> > > My morphological watershed filter has
> > >     input (double)
> > >     output (unsigned long)
> > >     SetMarkWatershedLine=false.
> > > My relabel component image filter has
> > >     input (unsigned long)
> > >     output (unsigned int)
> > > The relabeler outputs for my example are [1...342] which seems to be
> > > still
> > > well within the range of my output type.
> > >
> > > Albert
> > >
> > > ----- Original Message -----
> > > From: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>
> > > To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> > > Cc: <Richard.Beare at ieee.org>; <insight-users at itk.org>
> > > Sent: Thursday, February 08, 2007 1:48 AM
> > > Subject: Re: [Insight-users] Watershed Behavior
> > >
> > >
> > > Hi,
> > >
> > > You may also want to test the morphological watershed Richard and I have
> > > contributed, and see if it gives better results.
> > >
> > > http://hdl.handle.net/1926/202
> > >
> > > You can also found this new filter in ITK cvs now.
> > >
> > > Regards,
> > >
> > > Gaetan
> > >
> > >
> > > On Thu, 08 Feb 2007 04:34:39 +0100, Richard Beare
> > > <richard.beare at gmail.com> wrote:
> > >
> > > > Have a look at the gradient image and dheck whether there are plateaus
> > > > in the zig-zag area. The behaviour of the standard itk watershed is
> > > > somewhat arbitary in the presence of plateaus.
> > > >
> > > >
> > > > On 2/8/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > > >>
> > > >>
> > > >> Dear experts
> > > >>
> > > >> I was just playing with the watershed pipeline a few days ago using a
> > > >> checkerboard pattern (with uint8 grids of black=64, gray=153,
> > > >> white=192),
> > > >> and observed a zig-zaggy pattern on some edges (see
> > > >> http://www.ece.ubc.ca/~alberth/watershed.png). Adding a
> > > >> smooth field on the checkboard results in more zig-zaggy behaviors on
> > > >> edges
> > > >> that seem fairly strong in the input image. I am wondering if this is
> > > >> normal
> > > >> behavior for the itkWatershedImageFilter?
> > > >>
> > > >> My pipeline (ITK 3.0.1) setup is as below:
> > > >>     file reader ->
> > > >>     vector gradient magnitude image filter (pca off) ->
> > > >>     watershed (level=0.2, threshold=0.0) ->
> > > >>     relabel component
> > > >>
> > > >> p.s. The black regions in the outputs are colormap problems and not a
> > > >> watershed issue. =)
> > > >>
> > > >> Thanks
> > > >> Albert
> > > >>
> > > >> _______________________________________________
> > > >> Insight-users mailing list
> > > >> Insight-users at itk.org
> > > >> http://www.itk.org/mailman/listinfo/insight-users
> > > >>
> > > >>
> > > > _______________________________________________
> > > > Insight-users mailing list
> > > > Insight-users at itk.org
> > > > http://www.itk.org/mailman/listinfo/insight-users
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > >
> >
>