[Insight-users] Output of the atlas segmentation.

[Lydia Ng]

>> 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.=20
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.
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> Yasser,
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> 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.
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> You should be ok using any atlas for your segmentation,
> via demons deformable registration.
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> Regards,
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>    Luis
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> ---------------------
> 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
> >>
> >>
> >>
> >>---------------------
> >>yasser salman wrote:
> >>
> >>>hi luis..
> >>>Is the output af atlas segmentation application is
> >>>only the validation study .., i mean the Results
> >>
> >>of
> >>
> >>>this application only i found
> >>>it in Result directory? if yes is there any
> >>>application( or modification) can i use to
> >>
> >>produced
> >>
> >>>segmented output images based on the atlas
> >>>segmentation? and i'll use these output files to
> >>>visualize it using VTK..
> >>>thanks..,
> >>>yasser
> >>>
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