[Insight-users] another question on FEM Registration
b gises
magicgises at yahoo.com
Sat, 20 Mar 2004 08:55:03 -0800 (PST)
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hi Luis,
Thanks for your advice, guess this workload is too much for the time constraint....actually i just need someone to tell me that (or else i wouldn't give up) ...So now, i think i better use some of the implented applications in ITK, hope i'll get your help as i progress. I think i'll start with SNAP, should i perform the segmentation for the long axis and short axis separately or try to register the images from these 2 perpendicular planes.
Thanks again and again
Best Regards
janiv
Luis Ibanez <luis.ibanez at kitware.com> wrote:
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" /* 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*
> - More reliable, more storage, less spam
>
Do you Yahoo!?
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<DIV>hi Luis,</DIV>
<DIV> </DIV>
<DIV>Thanks for your advice, guess this workload is too much for the time constraint....actually i just need someone to tell me that (or else i wouldn't give up) ...So now, i think i better use some of the implented applications in ITK, hope i'll get your help as i progress. I think i'll start with SNAP, should i perform the segmentation for the long axis and short axis separately or try to register the images from these 2 perpendicular planes.</DIV>
<DIV> </DIV>
<DIV>Thanks again and again</DIV>
<DIV>Best Regards</DIV>
<DIV>janiv</DIV>
<DIV><BR><B><I>Luis Ibanez <luis.ibanez at kitware.com></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR>Hi Janiv,<BR><BR>After looking at the scope of your project<BR>it seems that you are underestimating the<BR>effort required for achieving these goals.<BR><BR>If you are still getting familiar with<BR>programming, it is unlikely that you will<BR>be able to finish all these tasks in two<BR>months. This workload could easily be a PhD<BR>dissertation.<BR><BR>You may want to reconsider the scope of your<BR>project and start by solving a sub-set of the<BR>tasks.<BR><BR><BR>Regards,<BR><BR><BR><BR>Luis<BR><BR><BR><BR>--------------<BR>b gises wrote:<BR>> Hi Luis and James,<BR>> <BR>> Thanks for the detailed explanation on this FEM registration filter. <BR>> Well, i'm totally new to itk and only a beginner in programming (the <BR>> worst thing is that i've only a couple of months to do this), so i'm <BR>> looking into ways which i can reach the objective of the project:
1) <BR>> segment the right ventricle 2) mesh the model (prefably using the <BR>> tagged points as the nodes) 3) track the displacement of the tagged <BR>> points 4) the images were taken in 2 perpendicular planes (short and <BR>> long axis), so i need a way to get the 3D displacement 5) Visualize the <BR>> model and run an animation of the model's deformation<BR>> 6) if possible create a GUI for this problem.<BR>> <BR>> Can you briefly state any ways or examples which will be useful for me <BR>> to handle this problem.( i've built ITK, ITK Applications, VTK, FLTK)<BR>> <BR>> Thanks again and enjoy the weekend<BR>> Regards<BR>> janiv<BR>> <BR>> <BR>> <BR>> */"Gee, James" <GEEJAMES at UPHS.UPENN.EDU>/* wrote:<BR>> <BR>> just to follow up on luis's useful comments. in FEM, unlike finite<BR>> difference methods, the solution, although obtained at the mesh<BR>> nodes, is actually based on the entire (image) domain. it's<BR>>
intuitive to think of applying forces at mesh nodes but this doesn't<BR>> happen in the naive way we might think; instead, the solution at the<BR>> node embodies information from all the elements that contain this<BR>> node. this fundamentally distinguishes the approach from finite<BR>> difference techniques which is what is used to implement the Demons<BR>> non-rigid image registration capability that is also available in<BR>> ITK (this is also described in the upcoming Theory book).<BR>> <BR>> about physical models, this is in part related to the<BR>> deformation/penalty energy term in the registration formulation. <BR>> folks do indeed attempt to create physically plausible models for<BR>> registration/tracking/deformation modeling, and if you're interested<BR>> in this direction, then the underlying FEM framework of the<BR>> registration filter will be convenient for you. the current filter<BR>> available in the repository implements
various linear, so-called<BR>> small deformation models (this does NOT mean it will only<BR>> accommodate small image differences!). there is a new version that<BR>> includes large-deformation models, which is reported in a submitted<BR>> manuscript and should be checked in relatively soon.<BR>> <BR>> a word of caution: to fully exploit the capabilities of the<BR>> itkfemregistration filter requires, unfortunately, some significant<BR>> background on the user's part (in non-rigid registration, numerical<BR>> analysis, even non-linear continuum mechanics).<BR>> <BR>> <BR>> <BR>> <BR>> > -----Original Message-----<BR>> > From: Luis Ibanez [mailto:luis.ibanez at kitware.com]<BR>> > Sent: Friday, March 19, 2004 2:42 AM<BR>> > To: b gises<BR>> > Cc: insight-users at itk.org<BR>> > Subject: Re: [Insight-users] another question on FEM Registration<BR>> ><BR>> ><BR>> ><BR>> > Hi Janiv,<BR>>
><BR>> > The FEM-Based registration method is intended to be used<BR>> > for computing a deformation field over an image with the<BR>> > purpose of registering this image against another one.<BR>> ><BR>> > You could use this method for performing segmentation<BR>> > if you a lready had a segmented image and attempt to<BR>> > register it versus a new input image. This methodology<BR>> > is also known as 'atlas-based segmentation'.<BR>> ><BR>> > The mesh that the FEM method creates can have any shape,<BR>> > however by default, a regular grid is created. No meshing<BR>> > algorithms are provided in ITK. Meshing is in itself a hard<BR>> > enough problem.<BR>> ><BR>> > Once you manage to create your mesh, what the FEM method<BR>> > does is to compute forces on the mesh nodes. This forces<BR>> > are computed from the local displacement that you will have<BR>> > to apply to a
small image region surrounding the node in<BR>> > order to match the the intensities of the other image.<BR>> ><BR>> > From this local forces, and the assumption that the mesh is<BR>> > modeling a elastic body, the FEM method computes local<BR>> > displacements in all the mesh nodes. The displacements are<BR>> > then interpolated inside the mesh cells.<BR>> ><BR>> > The nodes in the FEM mesh are not used for segmentation, only<BR>> > for registration. They original positions are located with<BR>> > respect to the fixed image coordinate system.<BR>> ><BR>> > You will find a detailed description of this method in the<BR>> > Tutorial presentations:<BR>> ><BR>> > http://www.itk.org/HTML/Tutorials.htm<BR>> ><BR>> > in particular at<BR>> ><BR>> > <BR>> ><BR>> http://www.itk.org/CourseWare/Training/NonRigidRegistrationMethods.pdf<BR>> ><BR>> > you may find
useful to also look at<BR>> ><BR>> > <BR>> ><BR>> http://www.itk.org/CourseWare/Training/RegistrationMethodsOverview.pdf<BR>> ><BR>> ><BR>> > and of course at the SoftwareGuide<BR>> ><BR>> > http://www.itk.org/ItkSoftwareGuide.pdf<BR>> ><BR>> ><BR>> ><BR>> > If you manage to segment your cardiac image, you could<BR>> > create a Mesh from the segmentation and use it for<BR>> > representing the elastic body that is going to be deformed<BR>> > in order to match the other image.<BR>> ><BR>> > Note that this FEM Mesh doesn't have any real physical<BR>> > relationship with the cardiac tissue. That is, even if the<BR>> > Mesh is representing a physical model, this model is totally<BR>> > unrelated to the physical properties of the anatomic<BR>> > structures present in your image.<BR>> ><BR>> ><BR>> ><BR>> > Regards,<BR>> ><BR>>
><BR>> ><BR>> > Luis<BR>> ><BR>> ><BR>> ><BR>> > ---------------------------<BR>> > b gises wrote:<BR>> ><BR>> > > hi,<BR>> > > <BR>> > > This is another mail from the previous one on fem<BR>> > registration filter.<BR>> > > i have 10 time frames of tagged cardiac images, where i have to<BR>> > > extract a mesh of the right ventricle. Is it acceptable<BR>> > that i use the<BR>> > > itkfemregistration filter for the segmentation of th e right<BR>> > ventricle.<BR>> > > Does this filter perform registration of images on the<BR>> user-defined<BR>> > > nodes only, or on the whole image. I'm not sure if the<BR>> user-defined<BR>> > > nodes are for the segmentation and extraction of mesh, or for the<BR>> > > registration, or for both. i'm wondering if the nodes are<BR>> > placed just<BR>> > > on the fixed image,
or on both the fixed and moving image. If the<BR>> > > nodes have to be place on both images, then i suppose the nodes<BR>> are<BR>> > > used to extract the meshes for both images, and used to<BR>> > register the<BR>> > > nodes at time t0 to the nodes at time t1.......Can anyone please<BR>> > > explain to me about this filter, and if i can use this to create a<BR>> > > smooth meshed model of the right ventricle, and yet get the<BR>> > > displacement of the tagged points. Thank you very much<BR>> > > <BR>> > > regards<BR>> > > janiv<BR>> > ><BR>> ><BR>> ><BR>> ><BR>> > _______________________________________________<BR>> > Insight-users mailing list<BR>> > Insight-users at itk.org<BR>> > http://www.itk.org/mailman/listinfo/insight-> users<BR>> ><BR>> <BR>> Hi Luis and James,<BR>> <BR>> Thanks for the detailed explanation on
this FEM registration filter. <BR>> Well, i'm totally new to itk and only a beginner in programming (the <BR>> worst thing is that i've only a couple of months to do this), so i'm <BR>> looking into ways which i can reach the objective of the project: 1) <BR>> segment the right ventricle 2) mesh the model (prefably using the <BR>> tagged points as the nodes) 3) track the displacement of the tagged <BR>> points 4) the images were taken in 2 perpendicular planes (short and <BR>> long axis), so i need a way to get the 3D displacement 5) Visualize the <BR>> model and run an animation of the model's deformation<BR>> 6) if possible create a GUI for this problem.<BR>> <BR>> Can you briefly state any ways or examples which will be useful for me <BR>> to handle this problem.( i've built ITK, ITK Applications, VTK, FLTK)<BR>> <BR>> Thanks again and enjoy the weekend<BR>> Regards<BR>> janiv<BR>> <BR>> Do you Yahoo!?<BR>> *Yahoo! Mail*
<HTTP: mail.yahoo.com *http: mailtag_us us.rd.yahoo.com><BR>> - More reliable, more storage, less spam<BR>> <BR><BR><BR></BLOCKQUOTE><p><font face=arial size=-1>Do you Yahoo!?<br>
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