How to get contours from segmentation results?

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How to get contours from segmentation results?

zszhong
Hi there,

I'm a newbie of 3D slicer. Now I have a basic question.
I have obtained the 3D segmentation volumes (0 is background, 1 is tumor
object). Now I want to create a visualization for paper figure, are there
any ways to do this task in 3D Slicer?

I have tried the following two methods:
(1) using 3D canny edge detection
(https://www.mathworks.com/matlabcentral/fileexchange/45459-canny-edge-detection-in-2-d-and-3-d),
but the result looks bad.
(2) using the edge detection in 3D slicer, the result also look bad.

I want get a smoother 3D contour based on the 3D segmentation result. That
is, the 3D contour is the edge of the 3D segmentation.

Could you please give some advice? Any comments are greatly appreciated!
Thanks a lot!



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Re: How to get contours from segmentation results?

Andras Lasso-2

We moved all discussions to https://discourse.slicer.org. Please post your question there. Thank you!

 

Andras

 

From: [hidden email]
Sent: Wednesday, June 7, 2017 3:26 PM
To: [hidden email]
Subject: [slicer-users] How to get contours from segmentation results?

 

Hi there,

I'm a newbie of 3D slicer. Now I have a basic question.
I have obtained the 3D segmentation volumes (0 is background, 1 is tumor
object). Now I want to create a visualization for paper figure, are there
any ways to do this task in 3D Slicer?

I have tried the following two methods:
(1) using 3D canny edge detection
(https://www.mathworks.com/matlabcentral/fileexchange/45459-canny-edge-detection-in-2-d-and-3-d),
but the result looks bad.
(2) using the edge detection in 3D slicer, the result also look bad.

I want get a smoother 3D contour based on the 3D segmentation result. That
is, the 3D contour is the edge of the 3D segmentation.

Could you please give some advice? Any comments are greatly appreciated!
Thanks a lot!



--
View this message in context: http://slicer-users.65878.n3.nabble.com/How-to-get-contours-from-segmentation-results-tp4032281.html
Sent from the slicer-users mailing list archive at Nabble.com.
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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

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slicer-users or discourse

Robert Funnell
I keep seeing referrals from slicer-users to discourse.slicer.org but
the Slicer Web pages still instruct users to use slicer-users. Is that
going to be changed soon?

- Robert

On Thu, 8 Jun 2017, Andras Lasso wrote:

> We moved all discussions to https://discourse.slicer.org. Please post your question there. Thank you!
>
>
>
> Andras
>
>
>
> From: zszhong<mailto:[hidden email]>
> Sent: Wednesday, June 7, 2017 3:26 PM
> To: SPL Slicer Users<mailto:[hidden email]>
> Subject: [slicer-users] How to get contours from segmentation results?
>
>
>
> Hi there,
>
> I'm a newbie of 3D slicer. Now I have a basic question.
> I have obtained the 3D segmentation volumes (0 is background, 1 is tumor
> object). Now I want to create a visualization for paper figure, are there
> any ways to do this task in 3D Slicer?
>
> I have tried the following two methods:
> (1) using 3D canny edge detection
> (https://www.mathworks.com/matlabcentral/fileexchange/45459-canny-edge-detection-in-2-d-and-3-d),
> but the result looks bad.
> (2) using the edge detection in 3D slicer, the result also look bad.
>
> I want get a smoother 3D contour based on the 3D segmentation result. That
> is, the 3D contour is the edge of the 3D segmentation.
>
> Could you please give some advice? Any comments are greatly appreciated!
> Thanks a lot!
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/How-to-get-contours-from-segmentation-results-tp4032281.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
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Re: slicer-users or discourse

Steve Pieper-2
Yes, we are trying to transition but there are a lot of pages that may need updating - if you see any pages that point to the lists instead of the forum please let us know.

Adding to this thread would be a good place to list anything that still needs to be updated:


On Thu, Jun 8, 2017 at 8:48 AM, Robert Funnell <[hidden email]> wrote:
I keep seeing referrals from slicer-users to discourse.slicer.org but
the Slicer Web pages still instruct users to use slicer-users. Is that
going to be changed soon?

- Robert

On Thu, 8 Jun 2017, Andras Lasso wrote:

> We moved all discussions to https://discourse.slicer.org. Please post your question there. Thank you!
>
>
>
> Andras
>
>
>
> From: zszhong<mailto:[hidden email]>
> Sent: Wednesday, June 7, 2017 3:26 PM
> To: SPL Slicer Users<mailto:[hidden email]>
> Subject: [slicer-users] How to get contours from segmentation results?
>
>
>
> Hi there,
>
> I'm a newbie of 3D slicer. Now I have a basic question.
> I have obtained the 3D segmentation volumes (0 is background, 1 is tumor
> object). Now I want to create a visualization for paper figure, are there
> any ways to do this task in 3D Slicer?
>
> I have tried the following two methods:
> (1) using 3D canny edge detection
> (https://www.mathworks.com/matlabcentral/fileexchange/45459-canny-edge-detection-in-2-d-and-3-d),
> but the result looks bad.
> (2) using the edge detection in 3D slicer, the result also look bad.
>
> I want get a smoother 3D contour based on the 3D segmentation result. That
> is, the 3D contour is the edge of the 3D segmentation.
>
> Could you please give some advice? Any comments are greatly appreciated!
> Thanks a lot!
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/How-to-get-contours-from-segmentation-results-tp4032281.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
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[hidden email]
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