[Insight-users] Insight-users Digest, Vol 69, Issue 53

Thu Jan 14 14:52:09 EST 2010

> 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,

Maybe this will be useful to you:

http://wiki.slicer.org/slicerWiki/index.php/Modules:Simple_Region_Growing-Documentation-3.4

You can give a try to Slicer, and this can simplify your
experimentation with interactive segmentation.

AF

> 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
>> >>>>>>>
>> >>>>>>> _____________________________________
>> >>>>>>> Powered by www.kitware.com
>> >>>>>>>
>> >>>>>>> Visit other Kitware open-source projects at
>> >>>>>>> http://www.kitware.com/opensource/opensource.html
>> >>>>>>>
>> >>>>>>> Kitware offers ITK Training Courses, for more information visit:
>> >>>>>>> http://www.kitware.com/products/protraining.html
>> >>>>>>>
>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>> >>>>>>>
>> >>>>>>> Follow this link to subscribe/unsubscribe:
>> >>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>> >>>>>>>
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>
>> >>>
>> >>>
>> >>> _____________________________________
>> >>> Powered by www.kitware.com
>> >>>
>> >>> Visit other Kitware open-source projects at
>> >>> http://www.kitware.com/opensource/opensource.html
>> >>>
>> >>> Kitware offers ITK Training Courses, for more information visit:
>> >>> http://www.kitware.com/products/protraining.html
>> >>>
>> >>> Please keep messages on-topic and check the ITK FAQ at:
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>> >>>
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>> >>
>> >>
>> >>
>> >> --
>> >> Marco G.
>> >>
>> >>
>> >> _____________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
>> >> http://www.kitware.com/opensource/opensource.html
>> >>
>> >> Kitware offers ITK Training Courses, for more information visit:
>> >> http://www.kitware.com/products/protraining.html
>> >>
>> >> Please keep messages on-topic and check the ITK FAQ at:
>> >> http://www.itk.org/Wiki/ITK_FAQ
>> >>
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>> >>
>> >
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.html
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
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>> >
>>
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