[Insight-users] Histoligical images registration

[delphine.ribes at epfl.ch]

Thanks a lot for all this usefull information.

Delphine

Selon Luis Ibanez <luis.ibanez at kitware.com>:

>
> Hi Delphine,
>
>
> Thanks for preparing and posting the screen shots.
>
>
> I guess that you are using the LFBGSBOptimizer:
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1LBFGSBOptimizer.html
>
> If that's the case, you could use the bounds restriction
> to prevent the BSpline nodes that are over that patch
> (patch = the section that you want not to deform) from
> having values different from zero.
>
> Note that the ParametersArray of the transform, contains
> the components of the deformation vectors associated to
> every node of the BSpline grid. By limiting the values
> of deformation of some of those nodes you can restrict
> the deformation of some regions of the image.
>
> The drawback is that if you want to have fine control
> over the size and shape of the deformation, you may
> have to increase the size of the BSpline grid, and that
> has a linear impact on the computation time of the
> registration.
>
> You may want to start by (manually) drawing your
> BSpline grid on top of the image, in order to get
> a feeling of how precisely you could control the
> deformation of the external boundaries.
>
>
> ---
>
>
> An alternative approach is to use the FEM based
> deformable registration and to define landmarks.
>
> Another alternative approach is to modify the
> LevelSetMotionRegistration
>
http://www.itk.org/Insight/Doxygen/html/classitk_1_1LevelSetMotionRegistrationFilter.html
> where you could apply a mask to every iteration
> of the deformation field computation.
>
>
> You may also want to look at the following paper
> in the Insight Journal:
> http://insight-journal.org/dspace/handle/1926/549
> with the following reviews:
>
http://www.insight-journal.org/InsightJournalManager/view_reviews.php?back=publications.php%3Fjournalid%3D8%26order%3Drating%26revision_display%3Dcombined&pubid=156
>
>
>
>      Regards,
>
>
>         Luis
>
>
> -------------------------------
> delphine.ribes at epfl.ch wrote:
> > Hi luis,
> >
> > You can have a look at two screenshot of the images at the following
> location :
> > http://ltswww.epfl.ch/ltsftp/BeforeBspline.png
> > http://ltswww.epfl.ch/ltsftp/AfterBspline.png
> >
> > The red rectangle on the BeforeBspline.png images shows the external border
> > which should not be deformed as a part of the brain is missing.
> > The yellow rectangle on the AfterBslpine.png images shows the deformation.
> The
> > internal organ as the hippocampe is too deformed.
> >
> > So the region is located on the external border. To simplify the problem, I
> > would like to find a way to not deformed the external border. I already
> have a
> > mask of the images.
> >
> > Thanks a lot for all the help
> > Delphine
> >
> >
> > Selon Luis Ibanez <luis.ibanez at kitware.com>:
> >
> >
> >>
> >>Hi Delphine,
> >>
> >>There are various ways of preventing a region
> >>of the image from being deformed during the
> >>registration process.
> >>
> >>The appropriate method will depend on the location,
> >>size and shape of the region that you want to preserve.
> >>
> >>
> >>
> >>Questions:
> >>
> >>    What is the shape of this region ?
> >>
> >>    Is is a circular region in the middle of the image ?
> >>
> >>    Is it the external border of the image ?
> >>
> >>    Is it a rectangular region ?
> >>
> >>
> >>If you could post an explanatory diagram in a public web site,
> >>that will be great.
> >>
> >>
> >>   Thanks
> >>
> >>
> >>      Luis
> >>
> >>
> >>
> >>-------------------------------
> >>delphine.ribes at epfl.ch wrote:
> >>
> >>>Hi Luis,
> >>>
> >>>Thank you for the answer. But I would like to ask you another question. I
> >>
> >>am
> >>
> >>>looking for a way to tell the registration process to not deformed a part
> >>
> >>of
> >>
> >>>the image.
> >>>Right now I am using :
> >>>Bspline transform
> >>>LBFGS optmizer
> >>>Linear interpolator
> >>>and Normalized Correlation Metric
> >>>
> >>>Is there a way, using those parameters to tell not deformed this part ?
> >>>
> >>>Thanks a lot
> >>>Delphine
> >>>
> >>>
> >>>Selon Luis Ibanez <luis.ibanez at kitware.com>:
> >>>
> >>>
> >>>
> >>>>Hi Delphine,
> >>>>
> >>>>
> >>>>   Your registration problem sounds quite interesting.
> >>>>
> >>>>   One possible way of preventing the holes in the histological sample
> >>>>   from affecting the registration results is to take advantage of the
> >>>>   Masks.
> >>>>
> >>>>   You can define Masks in the Fixed image and in the Moving image
> >>>>   for selecting what pixels you want to participate in the
> >>>>   registration. If you create masks where the holes are excluded
> >>>>   from the mask, then the registration metric will be computed without
> >>>>   considering such holes.
> >>>>
> >>>>   It seems that you have already look at the ITK Software Guide
> >>>>
> >>>>             http://www.itk.org/ItkSoftwareGuide.pdf
> >>>>
> >>>>   in particular section 8.11.3
> >>>>   "Registration using masks constructed with Spatial Objects"
> >>>>   pdf-page 464-466.
> >>>>
> >>>>   What you want to do is to create Masks where all the pixels
> >>>>   corresponding to holes of the histological sample, are set to
> >>>>   Zero, and the others are set to non zero.  Note that you could
> >>>>   also take advantage of the mask to remove all the pixels outside
> >>>>   of the mouse body to count on the registration process. It is
> >>>>   usually advisable to leave a small border outside the body, as
> >>>>   a way of making sure the that transition between body and air
> >>>>   contributes to the registration process.
> >>>>
> >>>>
> >>>>   The trick now, is to find an easy way of building the Mask.
> >>>>   Hopefully the holes in your images are clear enough for using
> >>>>   simple segmentation methods.
> >>>>
> >>>>   If now, we may need to take a look at your images in order to
> >>>>   give you better advice.
> >>>>
> >>>>
> >>>>
> >>>>    Please let us know if you have more questions,
> >>>>
> >>>>
> >>>>        Thanks
> >>>>
> >>>>
> >>>>           Luis
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>------------------------------
> >>>>delphine.ribes at epfl.ch wrote:
> >>>>
> >>>>
> >>>>>Dear all,
> >>>>>
> >>>>>I am doing Image registration of histological images. My goal is to
> align
> >>>>
> >>>>brain
> >>>>
> >>>>
> >>>>>mice in the same space coordinate to compare them. To do so I am using a
> >>>>>reference volume.
> >>>>>During the sectioning, some part of the brain is lost which create
> holes.
> >>>>
> >>>>To
> >>>>
> >>>>
> >>>>>align volume, I am using 4 following registration : land mark, rigid,
> >>>>
> >>>>affine
> >>>>
> >>>>
> >>>>>and a non rigid one which is Bspline. the last one is used to align
> >>>>
> >>>>internal
> >>>>
> >>>>
> >>>>>organs. The alignment is good. But if the external border is cut,
> >>
> >>artifacts
> >>
> >>>>>appear.
> >>>>>
> >>>>>Do you know if there is a way to mask the hole to avoid those artifacts
> ?
> >>>>>
> >>>>>I read in the itk book that you can pass the mask to the metric, but as
> >>
> >>far
> >>
> >>>>as I
> >>>>
> >>>>
> >>>>>understand it, it helps to improve computational cost ( as the metric is
> >>>>>focusing on pixel mask).  But I might misunderstood it...
> >>>>>
> >>>>>Thanks a lot
> >>>>>Delphine
> >>>>>_______________________________________________
> >>>>>Insight-users mailing list
> >>>>>Insight-users at itk.org
> >>>>>http://www.itk.org/mailman/listinfo/insight-users
> >>>>>
> >>>>
> >>>
> >>>
> >
> >
> >
>