[Insight-users] automatic segmentation of bone in legs: which filter most suitable?

Thu Jan 14 12:09:26 EST 2010

Hi again,

I suppose that the Regiongrowing implemented in itk can also work in 3D
(correct me if I am wrong) and that means that once you specify a seed
within the bone, which is your main concern, it will automatically grow in
every direction and over all the slices until it reaches the borders.

Running the method in 2D (separately for each slice) I would not do it as
there may be discontinuities between two consecutive slices according to
where you place your seedpoint.

To my concern and looking at your image you only need two seed points: one
for the upper part of the knee (above the junction) and one for the lower
part (below the junction). At the end you will have  two separated piece of
leg-bone.

2010/1/14 michiel mentink <michael.mentink at st-hughs.ox.ac.uk>

>
> Well, the volume contains the knee within the boundaries. This means that
> at least
> the outer slices have "no knee" bits in them. If a seed would be placed
> there, then
> also "no knee" bits would be segmented as being "knee".
>
> I'm considering in making an interactive seed placing window that places
> seeds down
> all axes though, and give the user the option to remove seeds on the outer
> slices,
> so it was a good suggestion you gave.
>
> Michael
>
>
> On Thu, Jan 14, 2010 at 2:11 PM, Mark Roden <mmroden at gmail.com> wrote:
>
>> Hi Michael,
>>
>> Why not try seeding down some central axis in 3D?  Why do everything
>> one plane at a time, when you have a 3D volume already, and can just
>> use that?
>>
>> Mark
>>
>> On Thu, Jan 14, 2010 at 2:59 AM, michiel mentink
>> <michael.mentink at st-hughs.ox.ac.uk> wrote:
>> > I was playing around yesterday with the slice I posted to this thread.
>> >
>> > When placing one single seed, you can find the bone rather well, but
>> there
>> > is a big risk that the region spills over into the tissue surrounding
>> the
>> > bone.
>> > I haven't experimented yet with placing multiple seeds.
>> >
>> > If you look at the picture, you can see that the area surrounding the
>> > cartilage is delimiting the bone very well, but the side of the bone
>> does
>> > not produce
>> > sharp edges in the edge detect filter bit of this segmentation
>> algorithm.
>> >
>> > Also, I only tried one slice, and actually, I'd like to segment a
>> complete
>> > 3D volume of the bone. That means I have to place multiple seeds along
>> the
>> > bone and figure out some set of parameters that produces good results
>> for
>> > every slice.
>> >
>> > I'm a bit weary about this type of segmentation but I'll continue
>> > experimenting with it. Please let me know if you have
>> > hints/tips/suggestions/experiences
>> > regarding this.
>> >
>> > Michael
>> >
>> >
>> >
>> > On Wed, Jan 13, 2010 at 4:30 PM, marco giordano <marco.giord at gmail.com>
>> > wrote:
>> >>
>> >> Hi michiel,
>> >>
>> >> I am also involved in solving a similar problem so I am interested in
>> any
>> >> possible solution.
>> >>
>> >> I did not look at the values but it seems that the bones are well
>> >> delimited and also quite homogeneous.
>> >> If you can specify a seed easily (e.g by looking at the histogram) I
>> would
>> >> try with region growing first. The problem might be that the segmented
>> >> region overgrows if the borders are not sharp.
>> >>
>> >> Also watersheds should work but It will give you a complete
>> segmentation,
>> >> then you should select the region by yourself.
>> >>
>> >> Level sets may also be an option but it might be too much for this
>> case.
>> >>
>> >> I would be curious to see the results, please share any experience.
>> >>
>> >> Regards
>> >>
>> >>
>> >> 2010/1/12 michiel mentink <michael.mentink at st-hughs.ox.ac.uk>
>> >>>>>
>> >>>>> The images are made with MRI.
>> >>>>> You can see the two bones in the middle.
>> >>>>>
>> >>>>> Michael
>> >>>>>
>> >>>>>
>> >>>>> On Tue, Jan 12, 2010 at 3:10 PM, siqi chen <siqichensc at gmail.com>
>> >>>>> wrote:
>> >>>>>>
>> >>>>>> If you can post one sample image, that would be helpful to
>> determine
>> >>>>>> which filter is the appropriate one.
>> >>>>>>
>> >>>>>> Siqi
>> >>>>>>
>> >>>>>> On Tue, Jan 12, 2010 at 10:08 AM, michiel mentink
>> >>>>>> <michael.mentink at st-hughs.ox.ac.uk> wrote:
>> >>>>>>>
>> >>>>>>> Does anyone have experience with or know which segmentation
>> algorithm
>> >>>>>>> can be used
>> >>>>>>> best for segmenting bones in a knee?
>> >>>>>>>
>> >>>>>>> There are about 100 pages of segmentation algorithms in the ITK
>> >>>>>>> software guide..
>> >>>>>>>
>> >>>>>>> I have a DICOM volume I want to segment into a binary (labeled)
>> >>>>>>> volume and ultimately
>> >>>>>>> convert to a surface mesh of the individual bones.
>> >>>>>>>
>> >>>>>>> thanks, Michael
>> >>>>>>>
>> >>>>>>> _____________________________________
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>> >>>>>
>> >>>>>
>> >>>>
>> >>>
>> >>>
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>> >>
>> >>
>> >>
>> >> --
>> >> Marco G.
>> >>
>> >>
>> >> _____________________________________
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>> >
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>
>
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-- 
Marco Giordano
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