Create grayscale DICOM from segment

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Create grayscale DICOM from segment

kingcastle@gmx.net

Hello guys,

 

I’ve been playing around with various Features of Slicer and I have to say it is awesome. Great work and contributions from so many people.

 

Currently I’m working on a paper to unfold the kidney and I use the Robust Statistics Segmenter to get rid of the surrounding tissue.

This works great so far, but now i want to export the segmented area with the original grayscale values as dicom series.

I was able to export the output volume as dicom and I get the correct segmentet shape, but the grayscale values are lost.

 

Is there a way to create an output volume that uses the Information from the segment to create a segment with the original grayscale?

 

Regards

 

Philipp König

 

 

 

 


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Re: Create grayscale DICOM from segment

Andras Lasso-2

In Segmentations module export segments to a labelmap node. You can then use Mask Scalar Volume to clear regions of your grayscale volume.

 

What do you do with the masked images after you export them to DICOM?

 

Andras

 

From: [hidden email]
Sent: Saturday, December 3, 2016 9:24
To: [hidden email]
Subject: [slicer-users] Create grayscale DICOM from segment

 

Hello guys,

 

I’ve been playing around with various Features of Slicer and I have to say it is awesome. Great work and contributions from so many people.

 

Currently I’m working on a paper to unfold the kidney and I use the Robust Statistics Segmenter to get rid of the surrounding tissue.

This works great so far, but now i want to export the segmented area with the original grayscale values as dicom series.

I was able to export the output volume as dicom and I get the correct segmentet shape, but the grayscale values are lost.

 

Is there a way to create an output volume that uses the Information from the segment to create a segment with the original grayscale?

 

Regards

 

Philipp König

 

 

 

 


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Re: Create grayscale DICOM from segment

Gao, Yi
In reply to this post by kingcastle@gmx.net
Hi Philipp,

Do you mean you want to export the volume to DICOM as you showed in the screen shots? That is, when you later load the DICOM, you will see the kidney region in blue (or whatever masked region is colored)?

Best,
yi

On Sat, Dec 3, 2016 at 9:23 AM, [hidden email] <[hidden email]> wrote:

Hello guys,

 

I’ve been playing around with various Features of Slicer and I have to say it is awesome. Great work and contributions from so many people.

 

Currently I’m working on a paper to unfold the kidney and I use the Robust Statistics Segmenter to get rid of the surrounding tissue.

This works great so far, but now i want to export the segmented area with the original grayscale values as dicom series.

I was able to export the output volume as dicom and I get the correct segmentet shape, but the grayscale values are lost.

 

Is there a way to create an output volume that uses the Information from the segment to create a segment with the original grayscale?

 

Regards

 

Philipp König

 

 

 

 


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Re: Create grayscale DICOM from segment

kingcastle@gmx.net
In reply to this post by kingcastle@gmx.net

Thank you, the Mask Scalar Volume did the trick.

 

As DICOM I can import it into my tools which are written in java. I try to unfold it, similar to whats done with the skull here:

https://www.ncbi.nlm.nih.gov/pubmed/20332373

 

Regards

 

 

Von: [hidden email]
Gesendet: Samstag, 3. Dezember 2016 16:01
An: [hidden email]; [hidden email]
Betreff: RE: [slicer-users] Create grayscale DICOM from segment

 

In Segmentations module export segments to a labelmap node. You can then use Mask Scalar Volume to clear regions of your grayscale volume.

 

What do you do with the masked images after you export them to DICOM?

 

Andras

 

From: [hidden email]
Sent: Saturday, December 3, 2016 9:24
To: [hidden email]
Subject: [slicer-users] Create grayscale DICOM from segment

 

Hello guys,

 

I’ve been playing around with various Features of Slicer and I have to say it is awesome. Great work and contributions from so many people.

 

Currently I’m working on a paper to unfold the kidney and I use the Robust Statistics Segmenter to get rid of the surrounding tissue.

This works great so far, but now i want to export the segmented area with the original grayscale values as dicom series.

I was able to export the output volume as dicom and I get the correct segmentet shape, but the grayscale values are lost.

 

Is there a way to create an output volume that uses the Information from the segment to create a segment with the original grayscale?

 

Regards

 

Philipp König

 

 

 

 

 


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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