[Insight-users] Fwd: Re: Filling big 3D holes

[brian avants]

gib

another alternative is a topology preserving level set --- we have
this code available here

http://www.insight-journal.org/browse/publication/778

brian




On Wed, Feb 2, 2011 at 11:12 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> (sorry for forgetting to "reply-all")
>
> -------- Original Message --------
> Subject: Re: [Insight-users] Filling big 3D holes
> Date: Thu, 03 Feb 2011 17:04:25 +1300
> From: Gib Bogle <g.bogle at auckland.ac.nz>
> To: Richard.Beare at ieee.org
>
> Hi Richard,
>
> If I understand you correctly, the problem with the alternate method you
> suggest
> is that I cannot rely on the continuity of the vessel walls.  A vessel might
> be
> locally continuous, but there are always going to be holes in the walls
> somewhere in the vascular network, and some of the big vessels are riddled
> with
> holes.
>
> I spent some time trying to develop an algorithm for patching the gaps in
> the
> walls.  It works quite well, but unless it patches all the gaps it still
> doesn't
> enable application of a hole-filling algorithm based on connectivity.
>
> Thanks
> Gib
>
> On 3/02/2011 4:49 p.m., Richard Beare wrote:
>>
>> Hi,
>> There is a fillholes filter that is part of the binary attribute
>> morphology contribution. Alternatively, you can build a hole filler
>> using either connected component labelling or reconstruction
>> approaches. If you start with your binary image, label the non edge
>> intensity. Then throw away the label touching the image edge. The
>> remaining blobs should be the interior or your arteries. Combine these
>> with the original binary image to fill the holes.
>>
>> On Thu, Feb 3, 2011 at 2:28 PM, Gib Bogle<g.bogle at auckland.ac.nz>  wrote:
>>>
>>> I'm working with a volume image that was generated by labelling the
>>> laminae
>>> of blood vessels.  My aim is to segment out the vasculature.  There are
>>> many
>>> difficulties, and the particular issue I'm addressing at the moment is
>>> filling in the vessels.  The intensity of the labelling of the walls is
>>> variable, with patches that are indistinguishable from background.  The
>>> vessel diameters vary widely, from about 4 to about 60 voxels.  After
>>> some
>>> preprocessing I have a binary image, on which the ITK hole-filling
>>> function
>>> works well with the small-diameter vessels, but the big vessels present a
>>> problem, even when the walls are "watertight" (i.e. without holes).
>>>
>>> My best idea so far is to send probes out in all 26 directions (all
>>> neighbours of a voxel) and count the number of probes that hit a wall
>>> within
>>> a specified radius.  It's tricky to specify both the radius and the
>>> critical
>>> number of hits, without getting too many false positives (voxels outside
>>> the
>>> vessels showing up as inside).  (The filter is of course applied
>>> iteratively.)
>>>
>>> I'm wondering if anyone else here has addressed a similar problem.
>>>
>>> Thanks
>>> Gib
>>> _____________________________________
>>> 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:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>