[Insight-users] deformation of cardiac MR images

[Luis Ibanez]

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 prototype 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 consists 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
>