[Insight-users] Vessels Extraction

[Karthik Krishnan]

Hi Gianni,

The Curves2DExtractor application is more apt for vessel extraction from 
angiography images (there is a 3D counterpart that we committed 
recently, called Curves3DExtractor). The application, unlike the 
VesselExtraction.avi does not allow you to specify seed points since the 
vessel extraction is based on the hessian. The frustum spatial functions 
do give you some freedom with choosing parameters.

However if you are looking for vessel extraction using region growing 
techniques, Luis put together an application recently :    
InsightApplications/DuctExtractor, which is very nearly the same as what 
you see in the AVI. There isn't a webpage with pretty pictures for it, 
(unfortunately, I don't have "public" data to put up a webpage with 
pretty pictures for this application. If you can contrubute some, I can 
put up some/).

The application takes a 3D volume, computes the laplacian, followed by 
connected threshold segmentation with seed points.

To run the application:

1. Load the 3D volume,

2. Specify the number of iterations for smoothing ( curvature flow )

3. Generate the Laplacian. Here it is important to enter the approximate 
duct diameter (in physical units, This will be variance applied to the 
laplacian filter.). By selecting a large enough value, you can discard 
smaller vessels. 

4. Select seed points in the "Input image" along ducts you wish to segment

5. Choose an upper threshold . The threshold is chosen for the laplacian 
image. You can choose one by using the GUI to play with the window level 
settings of the laplacian and choosing the value on the lower bar that 
gives you a nearly binary image ( black duct against a bright background 
on the laplacian image )

6. Apply region growing (this uses connected threshold to segment the duct)


The application has been written to segment bright ducts against a 
darker brackground. So the threshold here is an upper threshold for the 
Connected Threshold algorithm. You could easily modify the application 
to specify a lower threshold if you have dark ducts against a bright 
background.

If you have any trouble using the application let us know.

HTH

Karthik






Gavin Baker wrote:

>Hi Gianni,
>
>
>On Tue, Aug 02, 2005 at 10:36:52PM +0200, Lazzarato Dott. Gianni wrote:
>
>  
>
>>                 could you please tell me if is there the code example of
>>the VesselExtraction.avi example I've found in itkDocuments \courseware
>>\training directory?
>>
>> Or someone can tell me how I can start and what itk filters I have to use
>>to reach similar result?
>>
>> 
>>
>>Your help will be very appreciate. Thanks a million.
>>    
>>
>
>To start with, have a look at the Curves2DExtractor program in
>InsightApplications.  It is described here:
>
>  http://www.itk.org/HTML/Curve2DExtraction.htm
>
>If you don't already have it, you can download the InsightApplications
>source from the usual place:
>
>  http://www.itk.org/HTML/Download.htm
>
>This technique uses a fairly typical approach, using a local Hessian to
>detect ridges.  Have a look at the papers by Stephen Aylward and Elizabeth
>Bullitt for a good description of vessel extraction, and citations of other
>related papers.
>
>ciao -
>
>  :: Gavin
>
>  
>