[Insight-users] another question on FEM Registration
wavelethe at pku.org.cn
wavelethe at pku.org.cn
Sat, 20 Mar 2004 22:55:26 +0800 (CST)
I am also paying attention on this subject.
and i am a graduate student on BME, after getting the bachelor degree of electronic science.
could you give me more advice? i just have one and a more little years before my graduation. I don't think i have mastered enough maths knowledge, such as FEM.
thx a lot for your kind help!
by the way, i test the deformableregistration1 using FiniteElementRegistrationParameters2.txt, but i don't know exactly what the meaning of the number for the landmark in the txt file.
i think the datas of each line are the corresponding points
for the first landmark, 2 means 2 dimensions, and the points are (3.0, 5,0) and (7.5, 7.6), (i am not sure the values are by pixel or by percent), and the weight value is 0.1, is it right?
<LoadLandmark>
% This is the first landmark
2 3.0 5.0 2 7.5 7.6 0.1
<LoadLandmark>
% This is the second landmark
2 23.0 35.0 2 27.5 37.6 0.1
<END>
> -----Original Message-----
> 发件人: Luis Ibanez <luis.ibanez at kitware.com>
> 日期: Sat, 20 Mar 2004 08:14:32 -0500
> 收件人: b gises <magicgises at yahoo.com>
> 抄送: "Gee, James" <GeeJames at uphs.upenn.edu>, insight-users at itk.org
> 主题: Re: [Insight-users] another question on FEM Registration
>
> Hi Janiv,
>
> After looking at the scope of your project
> it seems that you are underestimating the
> effort required for achieving these goals.
>
> If you are still getting familiar with
> programming, it is unlikely that you will
> be able to finish all these tasks in two
> months. This workload could easily be a PhD
> dissertation.
>
> You may want to reconsider the scope of your
> project and start by solving a sub-set of the
> tasks.
>
>
> Regards,
>
>
>
> Luis
>
>
>
> --------------
> b gises wrote:
> > Hi Luis and James,
> >
> > Thanks for the detailed explanation on this FEM registration filter.
> > Well, i'm totally new to itk and only a beginner in programming (the
> > worst thing is that i've only a couple of months to do this), so i'm
> > looking into ways which i can reach the objective of the project: 1)
> > segment the right ventricle 2) mesh the model (prefably using the
> > tagged points as the nodes) 3) track the displacement of the tagged
> > points 4) the images were taken in 2 perpendicular planes (short and
> > long axis), so i need a way to get the 3D displacement 5) Visualize the
> > model and run an animation of the model's deformation
> > 6) if possible create a GUI for this problem.
> >
> > Can you briefly state any ways or examples which will be useful for me
> > to handle this problem.( i've built ITK, ITK Applications, VTK, FLTK)
> >
> > Thanks again and enjoy the weekend
> > Regards
> > janiv
> >
> >
> >
> > */"Gee, James" <GeeJames at uphs.upenn.edu>/* wrote:
> >
> > just to follow up on luis's useful comments. in FEM, unlike finite
> > difference methods, the solution, although obtained at the mesh
> > nodes, is actually based on the entire (image) domain. it's
> > intuitive to think of applying forces at mesh nodes but this doesn't
> > happen in the naive way we might think; instead, the solution at the
> > node embodies information from all the elements that contain this
> > node. this fundamentally distinguishes the approach from finite
> > difference techniques which is what is used to implement the Demons
> > non-rigid image registration capability that is also available in
> > ITK (this is also described in the upcoming Theory book).
> >
> > about physical models, this is in part related to the
> > deformation/penalty energy term in the registration formulation.
> > folks do indeed attempt to create physically plausible models for
> > registration/tracking/deformation modeling, and if you're interested
> > in this direction, then the underlying FEM framework of the
> > registration filter will be convenient for you. the current filter
> > available in the repository implements various linear, so-called
> > small deformation models (this does NOT mean it will only
> > accommodate small image differences!). there is a new version that
> > includes large-deformation models, which is reported in a submitted
> > manuscript and should be checked in relatively soon.
> >
> > a word of caution: to fully exploit the capabilities of the
> > itkfemregistration filter requires, unfortunately, some significant
> > background on the user's part (in non-rigid registration, numerical
> > analysis, even non-linear continuum mechanics).
> >
> >
> >
> >
> > > -----Original Message-----
> > > From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
> > > Sent: Friday, March 19, 2004 2:42 AM
> > > To: b gises
> > > Cc: insight-users at itk.org
> > > Subject: Re: [Insight-users] another question on FEM Registration
> > >
> > >
> > >
> > > Hi Janiv,
> > >
> > > The FEM-Based registration method is intended to be used
> > > for computing a deformation field over an image with the
> > > purpose of registering this image against another one.
> > >
> > > You could use this method for performing segmentation
> > > if you a lready had a segmented image and attempt to
> > > register it versus a new input image. This methodology
> > > is also known as 'atlas-based segmentation'.
> > >
> > > The mesh that the FEM method creates can have any shape,
> > > however by default, a regular grid is created. No meshing
> > > algorithms are provided in ITK. Meshing is in itself a hard
> > > enough problem.
> > >
> > > Once you manage to create your mesh, what the FEM method
> > > does is to compute forces on the mesh nodes. This forces
> > > are computed from the local displacement that you will have
> > > to apply to a small image region surrounding the node in
> > > order to match the the intensities of the other image.
> > >
> > > From this local forces, and the assumption that the mesh is
> > > modeling a elastic body, the FEM method computes local
> > > displacements in all the mesh nodes. The displacements are
> > > then interpolated inside the mesh cells.
> > >
> > > The nodes in the FEM mesh are not used for segmentation, only
> > > for registration. They original positions are located with
> > > respect to the fixed image coordinate system.
> > >
> > > You will find a detailed description of this method in the
> > > Tutorial presentations:
> > >
> > > http://www.itk.org/HTML/Tutorials.htm
> > >
> > > in particular at
> > >
> > >
> > >
> > http://www.itk.org/CourseWare/Training/NonRigidRegistrationMethods.pdf
> > >
> > > you may find useful to also look at
> > >
> > >
> > >
> > http://www.itk.org/CourseWare/Training/RegistrationMethodsOverview.pdf
> > >
> > >
> > > and of course at the SoftwareGuide
> > >
> > > http://www.itk.org/ItkSoftwareGuide.pdf
> > >
> > >
> > >
> > > If you manage to segment your cardiac image, you could
> > > create a Mesh from the segmentation and use it for
> > > representing the elastic body that is going to be deformed
> > > in order to match the other image.
> > >
> > > Note that this FEM Mesh doesn't have any real physical
> > > relationship with the cardiac tissue. That is, even if the
> > > Mesh is representing a physical model, this model is totally
> > > unrelated to the physical properties of the anatomic
> > > structures present in your image.
> > >
> > >
> > >
> > > Regards,
> > >
> > >
> > >
> > > Luis
> > >
> > >
> > >
> > > ---------------------------
> > > b gises wrote:
> > >
> > > > hi,
> > > >
> > > > This is another mail from the previous one on fem
> > > registration filter.
> > > > i have 10 time frames of tagged cardiac images, where i have to
> > > > extract a mesh of the right ventricle. Is it acceptable
> > > that i use the
> > > > itkfemregistration filter for the segmentation of th e right
> > > ventricle.
> > > > Does this filter perform registration of images on the
> > user-defined
> > > > nodes only, or on the whole image. I'm not sure if the
> > user-defined
> > > > nodes are for the segmentation and extraction of mesh, or for the
> > > > registration, or for both. i'm wondering if the nodes are
> > > placed just
> > > > on the fixed image, or on both the fixed and moving image. If the
> > > > nodes have to be place on both images, then i suppose the nodes
> > are
> > > > used to extract the meshes for both images, and used to
> > > register the
> > > > nodes at time t0 to the nodes at time t1.......Can anyone please
> > > > explain to me about this filter, and if i can use this to create a
> > > > smooth meshed model of the right ventricle, and yet get the
> > > > displacement of the tagged points. Thank you very much
> > > >
> > > > regards
> > > > janiv
> > > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Insight-users mailing list
> > > Insight-users at itk.org
> > > http://www.itk.org/mailman/listinfo/insight-> users
> > >
> >
> > Hi Luis and James,
> >
> > Thanks for the detailed explanation on this FEM registration filter.
> > Well, i'm totally new to itk and only a beginner in programming (the
> > worst thing is that i've only a couple of months to do this), so i'm
> > looking into ways which i can reach the objective of the project: 1)
> > segment the right ventricle 2) mesh the model (prefably using the
> > tagged points as the nodes) 3) track the displacement of the tagged
> > points 4) the images were taken in 2 perpendicular planes (short and
> > long axis), so i need a way to get the 3D displacement 5) Visualize the
> > model and run an animation of the model's deformation
> > 6) if possible create a GUI for this problem.
> >
> > Can you briefly state any ways or examples which will be useful for me
> > to handle this problem.( i've built ITK, ITK Applications, VTK, FLTK)
> >
> > Thanks again and enjoy the weekend
> > Regards
> > janiv
> >
> > Do you Yahoo!?
> > *Yahoo! Mail* <http://us.rd.yahoo.com/mailtag_us/*http://mail.yahoo.com>
> > - More reliable, more storage, less spam
> >
>
>
>
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