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

Thu Jul 27 10:34:55 EDT 2017

You may also give elastix registration toolbox a try (http://elastix.isi.uu.nl/). It is based on ITK but it adds a number of registration classes. My experience is that with BRAINS you often need to tune parameters to get meaningful results, while elastix gives great results with default settings for all kinds of input data. Elastix is available in 3D Slicer, too (by installing SlicerElastix extension).

Andras

From: Community [mailto:community-bounces at itk.org] On Behalf Of Dženan Zukic
Sent: Thursday, July 27, 2017 10:22 AM
To: thanos thanos <thanosxania at gmail.com>
Cc: Insight-users <insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images

Hi Thanos,

segmentation is not a trivial task, and usually requires a lot of user intervention/interaction to achieve a satisfactory result.

Completely segmenting one case, and then registering other cases to the segmented one and transferring labels is called atlas segmentation.

To figure out proper registration parameters, you could play with BRAINSFit module of 3D Slicer (docs<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.slicer.org%2Fwiki%2FModules%3ABRAINSFit&data=02%7C01%7Classo%40queensu.ca%7C247a47ea85324d5a764c08d4d4fae8f1%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636367621488662816&sdata=k94xFtCvTDijsGhFfuDeRSSkeFeQFobaTtVJAOElxzE%3D&reserved=0>), which is built on top of ITK and provides a nice user interface with significant number of options to tweak.

For B-Splines, common number of grid points are up to maybe 13x13x13. Since you have a high frame rate, you would probably benefit from initializing registration of time point n+1 by resulting transform from time point n.

Regards,
Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Thu, Jul 27, 2017 at 8:08 AM, thanos thanos <thanosxania at gmail.com<mailto:thanosxania at gmail.com>> wrote:
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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