[Insight-users] vertebrae segmentation with GeodesicActiveContourShapePriorLevelSetFilter

Paul pare85 at googlemail.com
Fri Jun 25 05:59:24 EDT 2010 

Thank you very much for your comments, Juan.

Best regards,
Paul

> Giving a fast look at the results, I see the biggest problem on the
> upper side of the shape, in that zone the boundary term is not good to
> achieve the results, maybe increasing the weight of the shape term
> could help. In addition, on the lower part of the image it seems that
> the curve is attaching itself to the outer countour of the edge map
> (where the white zone starts), and not to the correct boundary (thin
> white countour). This could be because of the inflation (advection)
> term pushing the curve to go outside. To correct this, you could
> decrease the weight of the advection term, and/or shrinkig the initial
> countour to be slightly smaller than the desired shape, in order to
> have it inside of the object but very close.
> This trials could let know you if there is any set of parameters well
> suited for your image. I think that results are close, maybe will a
> little tailoring of the parameters you could get a decent
> segmentation. Again, I don't know the precision required in your
> application, so I can not tell if it is achievable with this
> technique.
> I hope these comments help you.
> Best regards,
>                     Juan
>
> On Wed, Jun 23, 2010 at 9:42 AM, Paul<pare85 at googlemail.com>  wrote:
>    
>> I set the desired final segmentation as initial condition. Here some new
>> pictures.
>>
>>
>> edge map:
>> http://250kb.de/xJNMujE
>>
>> new mean shape image and initial condition:
>> http://250kb.de/9FtvL84
>>
>> segmentation result:
>> http://250kb.de/Kwucded
>>
>> parameter
>>   - propagation 0.5
>>   - curvature 1
>>   - advection 3
>>   - shape 0.2
>>
>>
>> Regards
>> Paul
>>
>>
>> Am 21.06.2010 14:04, schrieb Juan Cardelino:
>>      
>>> One good thing to try, is to use the desired final segmentation as
>>> initial condition, and check if the evolution of the curve keeps it in
>>> place. One interesting thing to see is the edge map, if it is good
>>> enough it will tell you that you need less weight on the shape term.
>>> On the contrary, if the boundary map isn't good enough, maybe it is
>>> wise to raise the weight of the shape term.
>>> Could you please post the new results? It will be interesting to see
>>> how it goes.
>>> Regards,
>>>               Juan
>>>
>>> On Sun, Jun 20, 2010 at 6:25 PM, Paul<pare85 at googlemail.com>    wrote:
>>>
>>>        
>>>> Hello Juan,
>>>>
>>>> thank you for your prompt reply. You are right. The number of iterations
>>>> was
>>>> too small. The segmentation results are better now but they still aren' t
>>>> good enough. I will try some other parameter combinations, create a
>>>> better
>>>> mean shape image and check the edge image again. Maybe I can optimize
>>>> some
>>>> of this things.
>>>>
>>>> Best regards,
>>>> Paul
>>>>
>>>>
>>>>          
>>>>> Hey Paul,
>>>>> While I can't assure that this technique would work, I'm pretty
>>>>> confident that is a good path to follow. However, as they say, the
>>>>> devil is in the details, so maybe you will need some fine tuning to
>>>>> make it work.
>>>>> Regarding the particular problem with the results, I find interesting
>>>>> to see the final number of iterations in each case. It seems to me
>>>>> that your problem is that the default maximum number of iterations is
>>>>> too small. You can tell that because the front stop advancing in a
>>>>> quite arbritrary point, and not on an actual minimum of the energy.
>>>>> The second example only confirms my thesis, because the only thing you
>>>>> did is to increase the propagation speed, which partially aleviates
>>>>> the problem, but you are still stopping at an arbritrarly point. You
>>>>> can confirm this by looking at the console output of the program and
>>>>> see the final number of iterations. If that happens to be the problem,
>>>>> I suggest that you increase the number of iterations to a ridiculous
>>>>> number, like 10k, and see at what number it stops. It will be also
>>>>> useful if you post the output of the program.
>>>>> I wish you luck with the problem, and let us know how it turned out.
>>>>> Best regards,
>>>>>                      Juan
>>>>>
>>>>> On Sat, Jun 19, 2010 at 10:34 AM, Paul<pare85 at googlemail.com>      wrote:
>>>>>
>>>>>
>>>>>            
>>>>>> Hello mailinglist,
>>>>>>
>>>>>> I' m using the GeodesicActiveContourShapePriorLevelSetFilter to segment
>>>>>> 2D
>>>>>> ct data of vertebrae. I can't find the right parameters to get a good
>>>>>> segmentation of the typical vertebra shape. Do you think, it is
>>>>>> possible
>>>>>> to
>>>>>> get a good segmentation of vertebrae with the
>>>>>> GeodesicActiveContourShapePriorLevelSetFilter? The following links show
>>>>>> some
>>>>>> segmentation results, the input image and the mean shape image I'm
>>>>>> using.
>>>>>> Maybe you can give me some advice how I have to change the parameters.
>>>>>> I
>>>>>> tried some parameter combinations but did not get one satisfying
>>>>>> result.
>>>>>>
>>>>>> input image:
>>>>>> http://250kb.de/qJsgisV
>>>>>>
>>>>>> mean shape image:
>>>>>> http://250kb.de/e3leuKZ
>>>>>>
>>>>>> segmentation result with seed points: 3 propagation=2 advection=3
>>>>>> curvature=1 shape=0.5 distance=5
>>>>>>
>>>>>> http://250kb.de/oamCuus
>>>>>>
>>>>>> segmentation result with seed points: 5 propagation=4 advection=3
>>>>>> curvature=1 shape=0.5 distance=5
>>>>>>
>>>>>> http://250kb.de/KyAGhW7
>>>>>>
>>>>>>
>>>>>> Regards
>>>>>> Paul
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>>>>>>
>>>>>>
>>>>>>              
>>>>>
>>>>>            
>>>>
>>>>          
>>>
>>>        
>>
>>      
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