[Insight-users] Output of the atlas segmentation.

[yasser salman]

hi lydia..
thanx for these details.., one more question plz..,
is the output of the atlas_segmentation application is
volume of images type PNG. i see in file
SimpleAppOutput.txx use PGMVolumeWriter..
thanx..
yasser..

--- Lydia Ng <lng at insightful . com> wrote:
> >> can i use these data for  my own atlas-based
> > > segmentation?
> 
> Just to clarify:
> Do you mean if you could use one of the IBSR data as
> the moving (atlas)
> and another image from another all together
> different data set as the
> fixed (to be segmented) image?
> 
> If so, there are two issues you should be aware of:
> intensity matching
> and field of view.
> 
> Demons is basically "mean squares" type approach.
> That is it assume that
> pixel belonging to the same structure has the same
> intensity on both the
> moving and fixed images. So if you are using images
> from different
> scanners with different settings and protocol you
> will mostly likely
> need to preprocess the images so that the intensity
> matches.
> 
> In the application there is some preprocessing done
> with a
> HistogramMatchingImageFilter which tries to match
> intensity by matching
> the image histograms at specified number of points. 
> If you want to use images from different data sets,
> I strongly suggest
> that you read the reference for the histogram
> matching and know its
> limitations.
> 
> The other issue is the field of view, the classic
> demons algorithm
> assume that the structure in one image can be found
> in the other image.
> So if your two dataset have different field of views
> then the algorithm
> may also run into problems.
> 
> - Lydia
> 
> 
> > -----Original Message-----
> > From: Luis Ibanez [mailto:luis . ibanez at kitware . com]
> > Sent: Monday, August 18, 2003 12:03 PM
> > To: yasser salman
> > Cc: insight-users at public . kitware . com
> > Subject: Re: [Insight-users] Output of the atlas
> segmentation.
> > 
> > 
> > Yasser,
> > 
> > 
> > The fixed and moving image should have the same
> dimensions,
> > but not necessarily the same size. That is, both
> images
> > should be 2D, or both should be 3D. But the actual
> number
> > of pixels along each dimension may be different
> between the
> > two images.
> > 
> > You should be ok using any atlas for your
> segmentation,
> > via demons deformable registration.
> > 
> > 
> > Regards,
> > 
> > 
> >    Luis
> > 
> > 
> > ---------------------
> > yasser salman wrote:
> > > hi luis ..,
> > > yes u understand acutally what i mean..but how
> about
> > > the data??  i know in the DemonsRegistration the
> fixed
> > > images and moving image must have the same
> dimension
> > > ..,SO i have a Volume downloaded from IBSR
> > > (20Normal_T1 & 20Normal_T1_brain) which used in
> the
> > > atlas segmentaion application (IBSRValidation
> study in
> > > ITKApplication)
> > > can i use these data for  my own atlas-based
> > > segmentation? also i have a data from brain web
> > > (Simulated Brain Database)  found in
> > > www.bic.mni.mcgill.ca/brainweb.. how can i found
> the
> > > atlas to simulated brain Volume..? thanx Luis
> for ur
> > > helpfull support..
> > > yasser..
> > >
> > >
> > >
> > > --- Luis Ibanez <luis . ibanez at kitware . com> wrote:
> > >
> > >>Hi Yasser,
> > >>
> > >>
> > >>I'm not sure I understand your question...
> > >>It seems that you are interested in setting up
> > >>your own atlas-based segmentation procedure.
> > >>
> > >>
> > >>The essential class of the segmentation is the
> > >>DemonsRegistrationFilter
> > >>
> > >
> > >
> >
>
http://www . itk . org/Insight/Doxygen/html/classitk_1_1DemonsRegistrationFi
> lt
> > er.html
> > >
> > >>You may want to start by looking at the
> description
> > >>that Lydia made of this filter on the
> SoftwareGuide
> > >>
> > >>   http://www . itk . org/ItkSoftwareGuide . pdf
> > >>
> > >>    Section 8.13, pdf-page 318.
> > >>
> > >>The code is described there available at
> > >>
> > >
> > >
>
Insight/Examples/Registration/DeformableRegistraton2.cxx
> > >
> > >>The output of the Demons filter is a deformation
> > >>field
> > >>(an image of vectors).  You can use this
> deformation
> > >>field
> > >>as input to the itk::WarpImageFilter
> > >>
> > >
> > >
> >
>
http://public . kitware . com/Insight/Doxygen/html/classitk_1_1WarpImageFilt
> er
> > .html
> > >
> > >>and resample the moving image with it.
> > >>(this is illustrated in the example).
> > >>
> > >>If you used the atlas-image as the moving image
> on
> > >>the
> > >>registration process, then the warped
> moving-image
> > >>will
> > >>be equivalent to a segmentation of your data.
> > >>(your data to-be-segmented should have been the
> > >>fixed
> > >>image during the registration process).
> > >>
> > >>You may find simpler to modify the example that
> is
> > >>described in the software guide.
> > >>
> > >>
> > >>For visualizing your data using VTK, you simply
> need
> > >>to use the ImageToVTKImageFilter classes
> available
> > >>at
> > >>
> > >>     InsightApplications/Auxiliary/vtk
> > >>
> > >>and use the VTK class vtkImageViewer2.
> > >>
> > >
> > >
>
http://www . vtk . org/doc/release/4 . 2/html/classvtkImageViewer2 . html
> > >
> > >>
> > >>
> > >>Please let us know if you find any problems,
> > >>
> > >>
> > >>
> > >>    Thanks
> > >>
> > >>
> > >>
> > >>      Luis
> > >>
> 
=== message truncated ===


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