[ITK] [ITK-users] Pruning algorithm in tree structure

Fri Apr 22 11:28:06 EDT 2016

Hi Apantar,

that structure is not at all suitable for the algorithm I described. It
first needs to be converted into a tree data structure before the algorithm
I proposed can be applied to it. Starting with the root voxel of the tree,
you might want to use itk iterators to manually do BFS or DFS algorithms,
or use the already implemented filter for that, the FloodFillIterator
<http://www.itk.org/Doxygen/html/classitk_1_1FloodFilledImageFunctionConditionalIterator.html>
.

Regards

On Thu, Apr 21, 2016 at 9:58 PM, Apantar <2389127171 at qq.com> wrote:

> Hi Dženan,
>   It is so nice of you to be interested in my problem and help me like
> that. The skeleton is obtained through the Matlab,
>   so the type of data is double , the format is '.mat' and it is stored as
> a 512*512*452 volume.
>
> Regards
>
> ------------------ 原始邮件 ------------------
> *发件人:* "Dženan Zukić";<dzenanz at gmail.com>;
> *发送时间:* 2016年4月21日(星期四) 晚上9:23
> *收件人:* "Apantar"<2389127171 at qq.com>;
> *抄送:* "Insight-users"<insight-users at itk.org>;
> *主题:* Re: [ITK-users] Pruning algorithm in tree structure
>
> Hi Apantar,
>
> in which data structure is your airway skeleton?
>
> Regards
>
> On Wed, Apr 20, 2016 at 10:22 PM, Apantar <2389127171 at qq.com> wrote:
>
>> Hi Dženan,
>>
>> Thanks you very much. Your method is helpful and I can't help having a
>> try. But would you tell me which filter in ITK is appropriate in this
>> work?
>>
>> Regards,
>> Apantar
>> ------------------ 原始邮件 ------------------
>> *发件人:* "Dženan Zukić";<dzenanz at gmail.com>;
>> *发送时间:* 2016年4月20日(星期三) 晚上11:32
>> *收件人:* "Apantar"<2389127171 at qq.com>;
>> *抄送:* "Insight-users"<insight-users at itk.org>;
>> *主题:* Re: [ITK-users] Pruning algorithm in tree structure
>>
>> Hi Apantar,
>>
>> now the problem is clear to me. I would go about it like this:
>>
>> For each branch point calculate the distance from root, depth of left
>> branch and depth of right branch. If depth of one branch is much smaller
>> (<5%) than the other, eliminate it as noise. If you have diameter of the
>> airway at each segment of the tree, you can use it for even better results:
>> divide depth of each branch with the thickness at the branching point, and
>> if it is <1.5 thicknesses it is noise.
>>
>> Depth of branch=length of the deepest subbranch.
>>
>> Regards,
>> Dženan
>>
>> On Tue, Apr 19, 2016 at 10:39 PM, Apantar <2389127171 at qq.com> wrote:
>>
>>> Hi Dženan,
>>>
>>> Thanks for your reply. Now I get a already segmented airway tree and it
>>> is binary. Moreover, I get a binary skeleton of this airway tree.
>>> The airway tree and the skeleton are shown in the email attachment
>>> respectively. As shown in the picture of skeleton, there are many
>>> small branches which are caused by the noise or cavities on the main
>>> trachea. When your compare the airway tree with the skeleton, you may found
>>> this small
>>> branches on the main trachea are not the real part of the skeleton. So
>>> what can I do to prun this small branches.
>>>
>>> Regards,
>>> Apantar
>>> ------------------ 原始邮件 ------------------
>>> *发件人:* "Dženan Zukić";<dzenanz at gmail.com>;
>>> *发送时间:* 2016年4月19日(星期二) 晚上10:27
>>> *收件人:* "Apantar"<2389127171 at qq.com>;
>>> *抄送:* "insight-users"<insight-users at itk.org>;
>>> *主题:* Re: [ITK-users] Pruning algorithm in tree structure
>>>
>>> Hi Apantar,
>>>
>>> your description of the problem is not detailed enough (how about some
>>> screenshot? what are false branches on the centerline), and seems very open
>>> ended to give specific recommendation. Do you expect some algorithm which
>>> takes into account the underlying image, or just works with binary image?
>>> The latter seems like a either a very hard or a very easy problem. And the
>>> first seems like an ordinary airway extraction.
>>>
>>> Regards,
>>> Dženan
>>>
>>> On Mon, Apr 18, 2016 at 9:00 AM, Apantar <2389127171 at qq.com> wrote:
>>>
>>>> Hi，
>>>>   I have a binary skeleton of an airway tree but there are many false
>>>> branches on the centerline . So I wonder if there
>>>> is a filter in Itk which would be used to pruning the skeleton of the
>>>> airway tree.
>>>>
>>>> Thanks
>>>> Best Regards,
>>>> EVEN DUAN
>>>>
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>>
>
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