[Insight-users] Help needed for segmenting kidney with contrast agent

[koh kenny]

Hi ITK community members,

I'm currently a student trying to do segmentation on
medical images with ITK for the first time. But I had
problem segmenting the images. They are MR images
showing the kidney with contrast agent. The aim of the
segmentation is to segment NOT the whole kidney but
just part of the kidney with the contrast agent.

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Problem faced:
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Shape of those part with contrast agent are highly
iregular. The width of these highlighted region is
usually around few pixels wide (5~10), hence region
growing with NeighborhoodConnected with radius 1 will
either show leakage or terminate prematurely. With
ConfidenceConnected, leakage is also a major problem
since some of the edges blend with neighboring organs.
ThresholdConnected on the other hand gives redundant
regions even though major ROI are highlighted with
careful chosing of the 2 threshold values. 

I had initially wanted to use partly eroded image from
region growing as my inital contor for levelset.
However, it seems that getting this eroded image is
already giving me headache.

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Data
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I had uploaded the MR images together with the manual
segmented result by the doctor at my website. File is
in .zip format.

http://www.geocities.com/ophiophagus81/result_ZIP.zip

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Can anyone give me some idea how to approach this
problem (prefer in 3D)? Any inputs will be deeply
appreciated.
Thanks very much :)

Kenny


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