[Insight-users] ThresholdSegmentationLevelSet (itk)

[Luis Ibanez]

Abder,

If you open the image file with the ImageViewer application
(from InsightApplications) or any other viewer such as
ITK-SNAP, Slicer, VolView, or VV, you will be able to probe
the intensity values inside of the aorta, and you will find
that they are (+/- noise) around the level of 550.

You need an image viewer application to do this.
There are many choices, as you can see above.


     Luis



-------------
On Sun, Apr 1, 2012 at 1:23 PM, Abder-Rahman Ali
<abder.rahman.ali at gmail.com> wrote:
> Hi Luis,
>
> How did you conclude that the values of the aorta were around 550? Can
> someone use a histogram using ITK-SNAP? Is there some way?
>
> Thanks a lot.
>
> Abder-Rahman
>
> On Sun, Apr 1, 2012 at 4:30 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>
>> 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
>
>