from volume rendering to usable extracted files

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from volume rendering to usable extracted files

nicolasP
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Hello,

I am new at slicer, its potential seems impressive.

Actually I am looking for a way to perform automatic segmentation of the tracheo-bronchial tree and lung surface from DICOM data.
The volume rendering module seems to extract the information I need. Is that possible to go from the rendering to separate stl files (or point clouds) of the lung, the blood tree, the tracheo-bronchial tree?
I've been looking around but I didn't find any complete answer.

Thanks,
Nicolas
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Re: from volume rendering to usable extracted files

Steve Pieper-2
Hi Nicolas -

Volume rendering is just a display technique - to get an stl file you need to do segmentation and model building.  The links below may help.



Best,
Steve

On Tue, May 3, 2016 at 7:21 AM, nicolasP <[hidden email]> wrote:
<http://slicer-users.65878.n3.nabble.com/file/n4030361/lung_view.png> Hello,

I am new at slicer, its potential seems impressive.

Actually I am looking for a way to perform automatic segmentation of the
tracheo-bronchial tree and lung surface from DICOM data.
The volume rendering module seems to extract the information I need. Is that
possible to go from the rendering to separate stl files (or point clouds) of
the lung, the blood tree, the tracheo-bronchial tree?
I've been looking around but I didn't find any complete answer.

Thanks,
Nicolas




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Re: from volume rendering to usable extracted files

Murat Maga
In reply to this post by nicolasP
Hi Nicolas,

In the editor module you can segment the structures you wanted using the transfer function values as an approximate guide. There are utility tools that can help you with the segmentation process (such as island tool or levelset segmentation). You can then use the model maker module to create models of individual structures. As far as I know, you can't go directly from VR to models.

There might be domain specific tools for lung segmentation that  can speed up the process also.

HTH,
Murat

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of nicolasP
Sent: Tuesday, May 03, 2016 4:22 AM
To: SPL Slicer Users
Subject: [slicer-users] from volume rendering to usable extracted files

<http://slicer-users.65878.n3.nabble.com/file/n4030361/lung_view.png> Hello,

I am new at slicer, its potential seems impressive.

Actually I am looking for a way to perform automatic segmentation of the tracheo-bronchial tree and lung surface from DICOM data.
The volume rendering module seems to extract the information I need. Is that possible to go from the rendering to separate stl files (or point clouds) of the lung, the blood tree, the tracheo-bronchial tree?
I've been looking around but I didn't find any complete answer.

Thanks,
Nicolas




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Re: from volume rendering to usable extracted files

nicolasP
Hi,

thanks for your answers.
Ok, I will dug in those directions.

But I am still wondering, to perform volume rendering there is a need for
segmentation right? so this information should be somewhere?

best
Nicolas



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Re: from volume rendering to usable extracted files

nicolasP
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In reply to this post by Murat Maga
Hi,

thanks for your answers.
Ok, I will dug in those directions.

But I am still wondering, to perform volume rendering there is a need for segmentation right? so this information should be somewhere?

best
Nicolas
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Re: from volume rendering to usable extracted files

Kikinis, Ron,M.D.
In reply to this post by nicolasP
Hi Nicholas,

its in the transfer function. However, segmentations in Slicer are binary and transfer functions are not.

You can find the transfer function in the advanced section of the module in the tab called Volume properties. There is an icon at the top of the scalar opacity section that would allow you to set a rectangular transfer function. This way you could determine from the volume rendering, what threshold you would like.
HTH
Ron



On May 4, 2016, at 9:36 AM, nicolasP <[hidden email]> wrote:

Hi,

thanks for your answers.
Ok, I will dug in those directions.

But I am still wondering, to perform volume rendering there is a need for
segmentation right? so this information should be somewhere?

best
Nicolas



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-- 
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


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Re: from volume rendering to usable extracted files

Murat Maga
In reply to this post by nicolasP
VR is not segmentation. You can mimic segmentation to some extend by adjusting the opacity of scalar values in transfer function. But things are still connected and present in the dataset, just not displayed.  If your goal is just visualization, and VR seems to be doing a good job of isolating structures you want to study, you don't need to segment your dataset.  You can read more about VR at Wikipedia. https://en.wikipedia.org/wiki/Volume_rendering

M




-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of nicolasP
Sent: Wednesday, May 04, 2016 12:37 AM
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] from volume rendering to usable extracted files

Hi,

thanks for your answers.
Ok, I will dug in those directions.

But I am still wondering, to perform volume rendering there is a need for segmentation right? so this information should be somewhere?

best
Nicolas



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