How to identify coronaries in CTA?

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How to identify coronaries in CTA?

madanrao
Hello,

I am using vmtkSlicerModule to extract coronaries from a CTA but seems ending up with bronchi.

Are there any thumb rules that help physicians like me to identify right and left coronaries?

I have over two decades of experience in reading ECGs.

AM Mohan Rao

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Re: [slicer-users] How to identify coronaries in CTA?

madanrao
Hello Ron Kikinis,

Thanks.

My colleague has downloaded the dicom file for me from:

http://pubimage.hcuge.ch:8080/
TOUTATIX, was hosted by Michael Miyamoto MD of UCLA.

I resized it to 256x256 and extracted its subvolume.

I would try your suggestions and get back to you.

AM Mohan Rao

On Wed, Jan 27, 2010 at 5:48 PM, Ron Kikinis <[hidden email]> wrote:
Mohan,

If you can share an anonymized data set with me, I am happy to take a look. Some ideas:
-Use the  extract subvolume ROI module in the converters category to create a subvolme that contains little bronchi.
-Use the software ray casting in the volume rendering module to provide more anatomical context to the vessels that you have. That should make it easier to determine right and left. Alternately create a 3D model of the blood pool in the subvolume using the editor. That would be an alternate option to provide context.

Ron


On 1/27/10 4:27 AM, Madan Rao wrote:
Hello,

I am using vmtkSlicerModule to extract coronaries from a CTA but seems
ending up with bronchi.

Are there any thumb rules that help physicians like me to identify right
and left coronaries?

I have over two decades of experience in reading ECGs.

AM Mohan Rao



_______________________________________________
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

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


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Re: [slicer-users] How to identify coronaries in CTA?

Daniel Haehn
Hi Mohan,

I looked at your dataset and had the time to quickly give it a shot.

I did the following steps:

1. cut subvolume
2. VMTKVesselEnhancement with Sato's algorithm:
a) 1-4mm, 10 steps
b) line-like/plate-like: 0.5
c) blob-like: 500

3. VMTKEasyLevelSetSegmentation
a) Fast Marching initialization using one fiducial [-47.3,224.6,-216.21]
(I did not center the volume)
b) Threshold 129
c) Geodesic Active Contours
Inflation: 0
Curvature: 70
Advection: 100
Iterations: 10

Maybe this could be a starting point for you. Another hint might be to
use Target Points in the VMTKEasyLevelSetSegmentation module to prevent
leakage in the bronchi and surrounding tissue.

Bye,
Daniel

On Wed, 2010-01-27 at 19:10 +0530, Madan Rao wrote:

> Hello Ron Kikinis,
>
> Thanks.
>
> My colleague has downloaded the dicom file for me from:
>
> http://pubimage.hcuge.ch:8080/
> TOUTATIX, was hosted by Michael Miyamoto MD of UCLA.
>
> I resized it to 256x256 and extracted its subvolume.
>
> I would try your suggestions and get back to you.
>
> AM Mohan Rao
>
> On Wed, Jan 27, 2010 at 5:48 PM, Ron Kikinis <[hidden email]>
> wrote:
>         Mohan,
>        
>         If you can share an anonymized data set with me, I am happy to
>         take a look. Some ideas:
>         -Use the  extract subvolume ROI module in the converters
>         category to create a subvolme that contains little bronchi.
>         -Use the software ray casting in the volume rendering module
>         to provide more anatomical context to the vessels that you
>         have. That should make it easier to determine right and left.
>         Alternately create a 3D model of the blood pool in the
>         subvolume using the editor. That would be an alternate option
>         to provide context.
>        
>         Ron
>        
>        
>        
>         On 1/27/10 4:27 AM, Madan Rao wrote:
>        
>                
>                 Hello,
>                
>                 I am using vmtkSlicerModule to extract coronaries from
>                 a CTA but seems
>                 ending up with bronchi.
>                
>                 Are there any thumb rules that help physicians like me
>                 to identify right
>                 and left coronaries?
>                
>                 I have over two decades of experience in reading ECGs.
>                
>                 AM Mohan Rao
>                
>                
>                
>                
>                 _______________________________________________
>                 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
>        
>         --
>         Ron Kikinis, M.D.,
>         Professor of Radiology, Harvard Medical School
>         Director, Surgical Planning Laboratory
>         http://www.spl.harvard.edu/~kikinis
>
> _______________________________________________
> 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

_______________________________________________
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

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Re: How to identify coronaries in CTA?

madanrao
Hello Daniel,

Thanks.

I would work on both your and Ron's suggestions.

It would take quiet sometime for me to get there !

AM Mohan Rao

On Thu, Jan 28, 2010 at 12:56 AM, Daniel Haehn <[hidden email]> wrote:
Hi Mohan,

I looked at your dataset and had the time to quickly give it a shot.

I did the following steps:

1. cut subvolume
2. VMTKVesselEnhancement with Sato's algorithm:
a) 1-4mm, 10 steps
b) line-like/plate-like: 0.5
c) blob-like: 500

3. VMTKEasyLevelSetSegmentation
a) Fast Marching initialization using one fiducial [-47.3,224.6,-216.21]
(I did not center the volume)
b) Threshold 129
c) Geodesic Active Contours
Inflation: 0
Curvature: 70
Advection: 100
Iterations: 10

Maybe this could be a starting point for you. Another hint might be to
use Target Points in the VMTKEasyLevelSetSegmentation module to prevent
leakage in the bronchi and surrounding tissue.

Bye,
Daniel

On Wed, 2010-01-27 at 19:10 +0530, Madan Rao wrote:
> Hello Ron Kikinis,
>
> Thanks.
>
> My colleague has downloaded the dicom file for me from:
>
> http://pubimage.hcuge.ch:8080/
> TOUTATIX, was hosted by Michael Miyamoto MD of UCLA.
>
> I resized it to 256x256 and extracted its subvolume.
>
> I would try your suggestions and get back to you.
>
> AM Mohan Rao
>
> On Wed, Jan 27, 2010 at 5:48 PM, Ron Kikinis <[hidden email]>
> wrote:
>         Mohan,
>
>         If you can share an anonymized data set with me, I am happy to
>         take a look. Some ideas:
>         -Use the  extract subvolume ROI module in the converters
>         category to create a subvolme that contains little bronchi.
>         -Use the software ray casting in the volume rendering module
>         to provide more anatomical context to the vessels that you
>         have. That should make it easier to determine right and left.
>         Alternately create a 3D model of the blood pool in the
>         subvolume using the editor. That would be an alternate option
>         to provide context.
>
>         Ron
>
>
>
>         On 1/27/10 4:27 AM, Madan Rao wrote:
>
>
>                 Hello,
>
>                 I am using vmtkSlicerModule to extract coronaries from
>                 a CTA but seems
>                 ending up with bronchi.
>
>                 Are there any thumb rules that help physicians like me
>                 to identify right
>                 and left coronaries?
>
>                 I have over two decades of experience in reading ECGs.
>
>                 AM Mohan Rao
>
>
>
>
>                 _______________________________________________
>                 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
>
>         --
>         Ron Kikinis, M.D.,
>         Professor of Radiology, Harvard Medical School
>         Director, Surgical Planning Laboratory
>         http://www.spl.harvard.edu/~kikinis
>
> _______________________________________________
> 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


_______________________________________________
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[hidden email]
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Re: How to identify coronaries in CTA?

madanrao
Hello,

This a volume rendering of the same image:

Can we identify: bronchi, left coronaries (on the surface of heart) along with aorta, pulmonary trunk, vertebra, ribs and
left atrium in the attached picture?

I am wondering where pulmonary veins are.

AM Mohan Rao




On Thu, Jan 28, 2010 at 12:25 PM, Madan Rao <[hidden email]> wrote:
Hello Daniel,

Thanks.

I would work on both your and Ron's suggestions.

It would take quiet sometime for me to get there !

AM Mohan Rao


On Thu, Jan 28, 2010 at 12:56 AM, Daniel Haehn <[hidden email]> wrote:
Hi Mohan,

I looked at your dataset and had the time to quickly give it a shot.

I did the following steps:

1. cut subvolume
2. VMTKVesselEnhancement with Sato's algorithm:
a) 1-4mm, 10 steps
b) line-like/plate-like: 0.5
c) blob-like: 500

3. VMTKEasyLevelSetSegmentation
a) Fast Marching initialization using one fiducial [-47.3,224.6,-216.21]
(I did not center the volume)
b) Threshold 129
c) Geodesic Active Contours
Inflation: 0
Curvature: 70
Advection: 100
Iterations: 10

Maybe this could be a starting point for you. Another hint might be to
use Target Points in the VMTKEasyLevelSetSegmentation module to prevent
leakage in the bronchi and surrounding tissue.

Bye,
Daniel

On Wed, 2010-01-27 at 19:10 +0530, Madan Rao wrote:
> Hello Ron Kikinis,
>
> Thanks.
>
> My colleague has downloaded the dicom file for me from:
>
> http://pubimage.hcuge.ch:8080/
> TOUTATIX, was hosted by Michael Miyamoto MD of UCLA.
>
> I resized it to 256x256 and extracted its subvolume.
>
> I would try your suggestions and get back to you.
>
> AM Mohan Rao
>
> On Wed, Jan 27, 2010 at 5:48 PM, Ron Kikinis <[hidden email]>
> wrote:
>         Mohan,
>
>         If you can share an anonymized data set with me, I am happy to
>         take a look. Some ideas:
>         -Use the  extract subvolume ROI module in the converters
>         category to create a subvolme that contains little bronchi.
>         -Use the software ray casting in the volume rendering module
>         to provide more anatomical context to the vessels that you
>         have. That should make it easier to determine right and left.
>         Alternately create a 3D model of the blood pool in the
>         subvolume using the editor. That would be an alternate option
>         to provide context.
>
>         Ron
>
>
>
>         On 1/27/10 4:27 AM, Madan Rao wrote:
>
>
>                 Hello,
>
>                 I am using vmtkSlicerModule to extract coronaries from
>                 a CTA but seems
>                 ending up with bronchi.
>
>                 Are there any thumb rules that help physicians like me
>                 to identify right
>                 and left coronaries?
>
>                 I have over two decades of experience in reading ECGs.
>
>                 AM Mohan Rao
>
>
>
>
>                 _______________________________________________
>                 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
>
>         --
>         Ron Kikinis, M.D.,
>         Professor of Radiology, Harvard Medical School
>         Director, Surgical Planning Laboratory
>         http://www.spl.harvard.edu/~kikinis
>
> _______________________________________________
> 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



_______________________________________________
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

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