[Insight-users] deformation of cardiac MR images
s y
superhashbrown at yahoo.com.sg
Fri, 13 Feb 2004 17:17:38 +0800 (CST)
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Hi Luis and all,
i'm new to itk and image processing, so do bear with me as i'm still a little confused, and i hope to get the framework correct
so should i load the volume for short axis and long axis separately or process the whole (both short axis and long axis) volume?
Luis wrote:
>Notice that the FEM framework is used for
modeling the *image* as an elastic material,
and applying forces on it in order to deform
it and achieve registration. >
in that case what should i use for registration?
you mentioned deformable registration between 2 volumes..did you mean performing registration on the images (not the construted models) and obtain deformation field (did you mean that the result of the registration can produce dx, dy, dz.....or they are just for the sole purpose of image registration with no physical information for later use for strain calculations)
you also mentioned the need to segment and mesh the MR images to study the deformations...should i perform segmentation at time t0 or all the frames (what abt meshing, just for t0 or all frames)?
is this what i should do: 1) load volumetric images 2) enhance images 3) perform registration for image at time t(i) with t(i+1) 4) segment the volumetric image at t0 5) mesh the segmented volumetric image 6) use deformation field from registration part and apply to the the meshed model 7) write a c++ program to calculate strain
can you kindly list the steps (tools to consider and examples for each step) that i should adhere to for studying and visualizing this deformation, i really appreciate your help
Best Regards
jason
Luis Ibanez <luis.ibanez at kitware.com> wrote:
Hi Jason,
Yes, you probably want to load the full volume
corresponding to time t0 from the DICOM files.
Then load the volume corresponding to time t1,
perform deformable registration between these
two volumes, and obtain a deformation field.
Then you could take image for t1 and register it
with image for time t2, and in general register
image at time t(i) with the one at time t(i+1).
Notice that the FEM framework is used for
modeling the *image* as an elastic material,
and applying forces on it in order to deform
it and achieve registration. The deformations
produced are totaly artificial and lack any
physical meaning.
If you actually want to model the heart, you
could still use the FEM classes in ITK but
not in the sense of registration. You will
have to generate a mesh on the cardiac muscle
and then study the deformations. For meshing
the heart you probably need to segment it
from the MR images first.
Regards,
Luis
-----------------
s y wrote:
> Hi Luis,
>
> did you mean i should first load dicom slices as a single volume for the
> start of the cardiac cycle (t0) using the Dicom series reader, perform
> image enhancement, segmentation, FEM/landmarks/Bsplines etc. in 3D,
> then do registration for the rest of the volumetric images at different
> time instances like this:
>
> registrate the construted model for time t1 with volumetric images at
> time t2, then with that information, registrate with images at time t3,
> and so on...
>
> in the end, i would like to perform strain analysis, and calculate
> rotations of the left ventricular points during the cardiac cycle, so is
> FEM-based the best choice?
>
> Thanks for your help
>
> Best regards
> jason
>
>
>
> */Luis Ibanez /* wrote:
>
> Hi Jason,
>
>
> First you may want to get familiar with
> the process of loading DICOM slices as
> a single volume.
>
> For example look at
>
> Insight/Examples/IO/
> DicomSeriesReadImageWrite.cxx
>
>
> Then, you may want to look at the following
> options for deformable registration:
>
>
> 1) Demons, with landmarks initialization
> 2) BSplines transforms
> 3) FEM-Based.
>
> For (1) you may look first at getting familiar
> with the Landmark Warping example in
>
> Insight/Examples/Registration/
> LandmarkWarping2.cxx
>
> Since the MR tags will give you a natural
> framework for setting landmarks that can
> be used for initializing a deformation
> field.
>
> This deformation field can be use as input
> for any of the two the Demons registration
> filters.
>
> For Visualization,
> you certainly want to use VTK. A good way
> to p! rototype the visualization pipeline is
> to use ParaView (a free and open source tool).
>
> You can download ParaView from
>
> http://www.paraview.org/HTML/Index.html
>
> It can be used for visualizing your images
> and the deformation fields produced by the
> registration algorithms.
>
> Once you identify a convenient visualization
> pipeline, you can export it as a batch script
> and use it as such or translate it into C++.
>
>
> ParaView also offers functionalities for
> running animations of data sets.
>
>
> Note that if you want to see a surface model
> you will have to perform segmentation in
> at least one of the datasets. The segmentation
> can then be mapped into the other datasets
> using the corresponding deformation fields.
>
>
>
> Regards,
>
>
> Luis
>
>
>
>
> ----------------
> s y wrote:
>
> > Hi to all,
> >
> > i have a dataset of cardiac MR images in dicom format (with MR
> tagging)
> > which co! nsists of short and long axis slices for the whole of the
> > cardiac cycle
> > my objective is to reconstruct the volume of the heart (or a FEM
> model
> > of it) so as to view and analyse the deformation of the heart
> during the
> > cycle.
> >
> > i've built vtk, itk and fltk. However, i'm not sure what are the
> tools
> > to use and how to go about it.
> >
> > should i use itk to segment and registrate the images slice by
> slice for
> > each instance first, then use vtk to render it, or are there any
> better
> > ways to do it with vtk and itk? also, is it possible to create an
> > animation of the deformation of the model during the cycle?
> >
> > any suggestions are welcome
> > Thanks
> >
> > regards
> > jason
> >
>
>
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
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>
> - Get clicking with thousands of local singles today! /
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<DIV>
<DIV>Hi Luis and all,</DIV>
<DIV> </DIV>
<DIV>i'm new to itk and image processing, so do bear with me as i'm still a little confused, and i hope to get the framework correct</DIV>
<DIV>so should i load the volume for short axis and long axis separately or process the whole (both short axis and long axis) volume? </DIV>
<DIV> </DIV>
<DIV>
<DIV>Luis wrote:</DIV>
<DIV>>Notice that the FEM framework is used for<BR>modeling the *image* as an elastic material,<BR>and applying forces on it in order to deform<BR>it and achieve registration. ></DIV>
<DIV> </DIV>
<DIV>in that case what should i use for registration?</DIV>
<DIV> </DIV></DIV>
<DIV>you mentioned deformable registration between 2 volumes..did you mean performing registration on the images (not the construted models) and obtain deformation field (did you mean that the result of the registration can produce dx, dy, dz.....or they are just for the sole purpose of image registration with no physical information for later use for strain calculations)</DIV>
<DIV> </DIV>
<DIV>you also mentioned the need to segment and mesh the MR images to study the deformations...should i perform segmentation at time t0 or all the frames (what abt meshing, just for t0 or all frames)? </DIV>
<DIV> </DIV>
<DIV>is this what i should do: 1) load volumetric images 2) enhance images 3) perform registration for image at time t(i) with t(i+1) 4) segment the volumetric image at t0 5) mesh the segmented volumetric image 6) use deformation field from registration part and apply to the the meshed model 7) write a c++ program to calculate strain </DIV>
<DIV> </DIV>
<DIV>can you kindly list the steps (tools to consider and examples for each step) that i should adhere to for studying and visualizing this deformation, i really appreciate your help</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Best Regards</DIV>
<DIV>jason</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR><BR><BR> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR><B><I>Luis Ibanez <luis.ibanez at kitware.com></I></B> wrote: </DIV>
<BLOCKQUOTE class=replbq style="BORDER-LEFT: #1010ff 2px solid; MARGIN-LEFT: 5px; PADDING-LEFT: 5px"><BR>Hi Jason,<BR><BR>Yes, you probably want to load the full volume<BR>corresponding to time t0 from the DICOM files.<BR>Then load the volume corresponding to time t1,<BR>perform deformable registration between these<BR>two volumes, and obtain a deformation field.<BR><BR>Then you could take image for t1 and register it<BR>with image for time t2, and in general register<BR>image at time t(i) with the one at time t(i+1).<BR><BR>Notice that the FEM framework is used for<BR>modeling the *image* as an elastic material,<BR>and applying forces on it in order to deform<BR>it and achieve registration. The deformations<BR>produced are totaly artificial and lack any<BR>physical meaning.<BR><BR>If you actually want to model the heart, you<BR>could still use the FEM classes in ITK but<BR>not in the sense of registration. You will<BR>have to generate a mesh on the cardiac muscle<BR>and then study
the deformations. For meshing<BR>the heart you probably need to segment it<BR>from the MR images first.<BR><BR><BR><BR>Regards,<BR><BR><BR>Luis<BR><BR><BR>-----------------<BR>s y wrote:<BR><BR>> Hi Luis,<BR>> <BR>> did you mean i should first load dicom slices as a single volume for the <BR>> start of the cardiac cycle (t0) using the Dicom series reader, perform <BR>> image enhancement, segmentation, FEM/landmarks/Bsplines etc. in 3D, <BR>> then do registration for the rest of the volumetric images at different <BR>> time instances like this:<BR>> <BR>> registrate the construted model for time t1 with volumetric images at <BR>> time t2, then with that information, registrate with images at time t3, <BR>> and so on...<BR>> <BR>> in the end, i would like to perform strain analysis, and calculate <BR>> rotations of the left ventricular points during the cardiac cycle, so is <BR>> FEM-based the best choice?<BR>> <BR>> Thanks for your
help<BR>> <BR>> Best regards<BR>> jason<BR>> <BR>> <BR>> <BR>> */Luis Ibanez <LUIS.IBANEZ at KITWARE.COM>/* wrote:<BR>> <BR>> Hi Jason,<BR>> <BR>> <BR>> First you may want to get familiar with<BR>> the process of loading DICOM slices as<BR>> a single volume.<BR>> <BR>> For example look at<BR>> <BR>> Insight/Examples/IO/<BR>> DicomSeriesReadImageWrite.cxx<BR>> <BR>> <BR>> Then, you may want to look at the following<BR>> options for deformable registration:<BR>> <BR>> <BR>> 1) Demons, with landmarks initialization<BR>> 2) BSplines transforms<BR>> 3) FEM-Based.<BR>> <BR>> For (1) you may look first at getting familiar<BR>> with the Landmark Warping example in<BR>> <BR>> Insight/Examples/Registration/<BR>> LandmarkWarping2.cxx<BR>> <BR>> Since the MR tags will give you a natural<BR>> framework for setting landmarks that can<BR>> be used for initializing a deformation<BR>>
field.<BR>> <BR>> This deformation field can be use as input<BR>> for any of the two the Demons registration<BR>> filters.<BR>> <BR>> For Visualization,<BR>> you certainly want to use VTK. A good way<BR>> to p! rototype the visualization pipeline is<BR>> to use ParaView (a free and open source tool).<BR>> <BR>> You can download ParaView from<BR>> <BR>> http://www.paraview.org/HTML/Index.html<BR>> <BR>> It can be used for visualizing your images<BR>> and the deformation fields produced by the<BR>> registration algorithms.<BR>> <BR>> Once you identify a convenient visualization<BR>> pipeline, you can export it as a batch script<BR>> and use it as such or translate it into C++.<BR>> <BR>> <BR>> ParaView also offers functionalities for<BR>> running animations of data sets.<BR>> <BR>> <BR>> Note that if you want to see a surface model<BR>> you will have to perform segmentation in<BR>> at least one
of the datasets. The segmentation<BR>> can then be mapped into the other datasets<BR>> using the corresponding deformation fields.<BR>> <BR>> <BR>> <BR>> Regards,<BR>> <BR>> <BR>> Luis<BR>> <BR>> <BR>> <BR>> <BR>> ----------------<BR>> s y wrote:<BR>> <BR>> > Hi to all,<BR>> ><BR>> > i have a dataset of cardiac MR images in dicom format (with MR<BR>> tagging)<BR>> > which co! nsists of short and long axis slices for the whole of the<BR>> > cardiac cycle<BR>> > my objective is to reconstruct the volume of the heart (or a FEM<BR>> model<BR>> > of it) so as to view and analyse the deformation of the heart<BR>> during the<BR>> > cycle.<BR>> ><BR>> > i've built vtk, itk and fltk. However, i'm not sure what are the<BR>> tools<BR>> > to use and how to go about it.<BR>> ><BR>> > should i use itk to segment and registrate the images slice by<BR>> slice
for<BR>> > each instance first, then use vtk to render it, or are there any<BR>> better<BR>> > ways to do it with vtk and itk? also, is it possible to create an<BR>> > animation of the deformation of the model during the cycle?<BR>> ><BR>> > any suggestions are welcome<BR>> > Thanks<BR>> ><BR>> > regards<BR>> > jason<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>> / *Y! Asia presents Lavalife* <BR>> <BR>> - Get clicking with thousands of local singles today! /<BR>> <BR><BR><BR><BR>_______________________________________________<BR>Insight-users mailing list<BR>Insight-users at itk.org<BR><A href="http://www.itk.org/mailman/listinfo/insight-users">http://www.itk.org/mailman/listinfo/insight-users</A></BLOCKQUOTE></DIV><p><img
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