[ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images

[thanos thanos]

Hello everyone,

The past months I have been working on tasks of Segmentation and
Registration of 4D ultrasound images so I can eventually do a proper
Cardiac Deformation analysis. Unfortunately I am struggling on my own to
solve these problems so I still haven't found a proper workflow and this is
why I am posting here in case someone has a suggestion or a recommendation.

For the acquisition of my data, a pig heart was placed inside a water tank
with the 4D transducer on the bottom of the tank (the apex of the heart was
about 5 cm from the transducer) and with around 50 volumes per second I
obtained images of 120x90x80, that after masking I ended up with volumes of
75x70x52 (x,y,z).

So far, I use Curvature Anisotropic Diffusion using the ITK libraries in
order to perform an automatic segmentation using Active Contours (with
Matlab). I filtered my data, mostly to assist my 2D segmentation algorithm,
which I perform slice by slice on the z axis. I obtain a 3D model using the
isosurfaces.

Then I tried both the Demons registration and the Bsplines registration on
the 3D volumes. I tried both on the original (unsegmented) data and two
segmented volumes, but I can not say that I am quite satisfied with any of
the results.

So my questions are the following :
1) Is it necessary to perform segmentation before the registration since my
heart is placed in a water tank, so there are no other organs around?
2) Should the registration be done on the filtered or the unfiltered data?
3) I am not satisfied at all with my segmentation algorithm since active
contours are quite sensitive to noise and because of the nature of the data
I have to use different parameters for every 4-5 slices. Therefore I was
thinking to perform an almost manual segmentation on one volume and then
use registration for the segmentation of the rest (if that is necessary).
So I am now studying and trying to say if something like that is possible
(and especially on ITK). If someone knows something about it, I would be
happy to hear.
4) What would be a proper number of grid points for my 75x70x52 images,
when using the B-Splines registration?

I am sorry for the long post but I have been struggling for too long with
this problem and I would really appreciate any kind of help.

Best regards,
Thanos
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