[Insight-users] ThresholdSegmentationLevelSet (itk)

[Luis Ibanez]

Hi Abder


Your .cxx file had multiple bugs,
particularly in the use of the argv arguments.

Please find attached a fixed version.

A command observer has been added in order
to track the evolution of the level set.

If you plot the output, you will see that the
RMS value start converging towards 600
iterations.

The command line that I used to run it is.

./thresholdLS IM.mha output.mha 35 17 28 5 500 1000 1

That is

seed x,y,z =   35 17 28

initial radius = 5

lower threshold = 500
upper threshold = 1000

curvature scaling  = 1


The aorta in this image have values around 550,
and it is the brightest object in the image, so,
choosing a lower threshold of 500, and  a very
high upper threshold captures the aorta.


---

Lateral comments:


1) There is no such thing as the "best" value
    for any parameter in a segmentation.

    We can only find values that are "good enough"
    for the task that you are pursuing.

    The concept of "best value", or "best algorithm"
    is a distortion resulting from the decadent
    Publishing practices that had mislead the
    medical image community for many years,
    both in Journals and Conferences.

    Unfortunately it continues to be propagated
    in our field, as a way of making possible to
    run conferences the way competitions are
    run in State Fairs... it is sad... really sad.


2) Rating a segmentation is an exercise that
    only makes sense in the context of the
    application that you are going to give
    to the output segmentation.

     Is this to implant a stent in the aorta ?
     Is this to deliver radiation treatment ?
     Is this to measure the diameter ?



  Regards,


       Luis


-------------------------------------------------------------
On Fri, Mar 30, 2012 at 5:30 AM, Abder-Rahman Ali
<abder.rahman.ali at gmail.com> wrote:
> Hello,
>
> Sorry for bothering again...
>
> I just have a small question and thought you may have an idea on this,
> especially that I'm kind of new to segmentation.
>
> I'm using "ThresholdSegmentationLevelSet" on a 3D image as shown in the
> attached code. I also attached "IM.mha" which represents an ascending aorta.
>
> Please note that the seed point is (x=35, y=17,z=28).
>
> I just want to ask:
>
> - What would be the best choice of upper and lower thresholds?
> - What would be the best value for SetCurvatureScaling()?
> - If you want to rate how well this segmentation worked, how much will you
> give it on a scale of 1-10 (1:bad, 10=best)?
>
> Thanks a lot and apologize for my disturbance.
>
> Abder-Rahman
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