[Insight-users] Volview Adds more contours than needed

[Luis Ibanez]

Hi ITK-Stanford

There is something strange in your description of the
problem.  Adding contours in VolView should only generate
iso-level at a particular value. It will not select a
region that has an assigned value.

If what you did was to *label* the segmented images and
you assigned a label value of 182 to the aorta, and a
label value of 0 to the trachea then spurious contours may
appear around the trachea if the trachea has bordering
labels that are at values > 182.

Keep in mind that when you ask for an iso-contours at level
182 what you are computing is a surface with values < 182
in one side and values > 182 on the other side. You are not
asking for the surface surrounding a region whose value is 182.



Here is a simple solution for your problem:

                     Use the ITK plugins in VolView.

Simply load your stack of images, then go to the menu

                    "View" -> "Filter"

and select the group

                 "Segmentation - Region Growing"

Then the filter

                 "Confidence Connected (ITK)"

Set

the number of iterations to 2
the multiplier to 1.0
the output value to 255

Then go to the menu

                  "View" -> "Markers"

enable "Display 3D cursor" and "Display 3D markers"

Add a 3D marker inside the structure that you want to
contour.

Then go back to the filters menu (there should be a
tab for it now) and click in "Apply Filter" the
segmentation result will be a binary image of your
label (eg. the region at label value 182 if that's
where you put the 3D marker).  Once there, you can
enable a contour at value level 128.

You will also find useful to run the AntiAlias image
filter available in the group " Surface Generation"
it will smooth the iso-surface of your binary segmenation
by reducing the staircase effects of the typical binary
images.


Please let us know if you find any problems,


Thanks


    Luis


--------------------------------------------------------
ITK Stanford wrote:

>  
> Hi,
>  
> I have a stack of .pgm files containing a segmented volume of the 
> heart.  I can open and view the intensity values of pixels in volview.  
> However, adding a contour at a certain intensity value, adds contours  
> for that value and all values lower than it.  For example the intensity 
> value of the descending aorta is 182 and the intensity value of trachea 
> is 0.  However adding a contour at value 182 also adds a contour at value 0.
>  
> Any idea why this is happening and how can it be fixed??
>  
> All help will be appreciated
> --
>