Phantom for SlicerIGT regisration

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Phantom for SlicerIGT regisration

barrett.anderies@asu.edu
Hello all,

I am trying to use Slicer with a Polaris Vicra optical tracking camera through the SlicerIGTI extension for my senior engineering project. I am a new to Slicer, and am still trying to learn its features. I have managed to configure my PLUS Server to send the appropriate data to the SlicerIGT OpenIGTLink client, and have visualized tool positions in the 3D view of Slicer. However, I am now faced with registering a phantom for testing. I was hoping to get some advice about the best way to do this. I am operating on a small budget, so I might not be able to get an MRI scan of something with fiducial markers. However, I do have access to a high end 3D printer, so if I could obtain a DICOM of any object with fiducial, I could 3D print a full scale mode of this DICOM. This video shows an example of what I am trying to do: https://www.youtube.com/watch?v=R3ROA94bbOg. Does anyone in the Slicer community have a DICOM of an object or patient (anonymized) with fiducials that they would be willing to share with me? Does anyone have any suggestion? As far as I understand, SlicerIGT only supports fiducial registration. If I could find a way to use a registration method that allows tracing of anatomy with a stylus to collect points, I could use any DICOM from my lab. Does SlicerIGT support anatomy-based registration (like that used by the Medtronic StealthStation)?

Thanks and best regards,

Barrett

--
Barrett Anderies
B.S.E. Biomedical Engineering | B.S. Mathematics
Barrett, the Honors College | Arizona State University
Phone: 480-721-9370
           [hidden email]

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Re: Phantom for SlicerIGT regisration

Andras Lasso-2

You can use any DICOM data, no need to have fiducial markers in the image. You can either do landmark registration or surface registration, both supported by SlicerIGT extension.

 

Landmark registration is simple, fast, and robust, so we use that for patient registration most of the time. You can either use anatomical landmarks (points that you can identify in the image and on the surface of the 3D-printed phantom) or draw a few divots in the segment editor.

 

For surface registration, you can collect points using Collect fiducials module and register using Fiducials-model registration module. Fiducials-model registration module requires a good initial guess, you can get that from either manual alignment or landmark registration.

 

See SlicerIGT tutorials for step-by-step instructions:

http://www.slicerigt.org/wp/user-tutorial/

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: February 16, 2017 11:47
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Phantom for SlicerIGT regisration

 

Hello all,

 

I am trying to use Slicer with a Polaris Vicra optical tracking camera through the SlicerIGTI extension for my senior engineering project. I am a new to Slicer, and am still trying to learn its features. I have managed to configure my PLUS Server to send the appropriate data to the SlicerIGT OpenIGTLink client, and have visualized tool positions in the 3D view of Slicer. However, I am now faced with registering a phantom for testing. I was hoping to get some advice about the best way to do this. I am operating on a small budget, so I might not be able to get an MRI scan of something with fiducial markers. However, I do have access to a high end 3D printer, so if I could obtain a DICOM of any object with fiducial, I could 3D print a full scale mode of this DICOM. This video shows an example of what I am trying to do: https://www.youtube.com/watch?v=R3ROA94bbOg. Does anyone in the Slicer community have a DICOM of an object or patient (anonymized) with fiducials that they would be willing to share with me? Does anyone have any suggestion? As far as I understand, SlicerIGT only supports fiducial registration. If I could find a way to use a registration method that allows tracing of anatomy with a stylus to collect points, I could use any DICOM from my lab. Does SlicerIGT support anatomy-based registration (like that used by the Medtronic StealthStation)?

 

Thanks and best regards,

 

Barrett


--

Barrett Anderies

B.S.E. Biomedical Engineering | B.S. Mathematics

Barrett, the Honors College | Arizona State University

Phone: 480-721-9370

           [hidden email]


_______________________________________________
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: Phantom for SlicerIGT regisration

Tamas Ungi-2

I think you could use any natural corner point as a fiducial. If you look at the landmark registration and surface registration tutorials at the slicerigt website you will see that those models don't have fiducials either.

Sent from my phone



From: slicer-users <[hidden email]> on behalf of Andras Lasso <[hidden email]>
Sent: Thursday, February 16, 2017 12:28:17 PM
To: [hidden email]; SPL Slicer Users
Subject: Re: [slicer-users] Phantom for SlicerIGT regisration
 

You can use any DICOM data, no need to have fiducial markers in the image. You can either do landmark registration or surface registration, both supported by SlicerIGT extension.

 

Landmark registration is simple, fast, and robust, so we use that for patient registration most of the time. You can either use anatomical landmarks (points that you can identify in the image and on the surface of the 3D-printed phantom) or draw a few divots in the segment editor.

 

For surface registration, you can collect points using Collect fiducials module and register using Fiducials-model registration module. Fiducials-model registration module requires a good initial guess, you can get that from either manual alignment or landmark registration.

 

See SlicerIGT tutorials for step-by-step instructions:

http://www.slicerigt.org/wp/user-tutorial/

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: February 16, 2017 11:47
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Phantom for SlicerIGT regisration

 

Hello all,

 

I am trying to use Slicer with a Polaris Vicra optical tracking camera through the SlicerIGTI extension for my senior engineering project. I am a new to Slicer, and am still trying to learn its features. I have managed to configure my PLUS Server to send the appropriate data to the SlicerIGT OpenIGTLink client, and have visualized tool positions in the 3D view of Slicer. However, I am now faced with registering a phantom for testing. I was hoping to get some advice about the best way to do this. I am operating on a small budget, so I might not be able to get an MRI scan of something with fiducial markers. However, I do have access to a high end 3D printer, so if I could obtain a DICOM of any object with fiducial, I could 3D print a full scale mode of this DICOM. This video shows an example of what I am trying to do: https://www.youtube.com/watch?v=R3ROA94bbOg. Does anyone in the Slicer community have a DICOM of an object or patient (anonymized) with fiducials that they would be willing to share with me? Does anyone have any suggestion? As far as I understand, SlicerIGT only supports fiducial registration. If I could find a way to use a registration method that allows tracing of anatomy with a stylus to collect points, I could use any DICOM from my lab. Does SlicerIGT support anatomy-based registration (like that used by the Medtronic StealthStation)?

 

Thanks and best regards,

 

Barrett


--

Barrett Anderies

B.S.E. Biomedical Engineering | B.S. Mathematics

Barrett, the Honors College | Arizona State University

Phone: 480-721-9370

           [hidden email]


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[hidden email]
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Re: Phantom for SlicerIGT regisration

barrett.anderies@asu.edu
In reply to this post by barrett.anderies@asu.edu
Hello Andras,

Excellent, thank you for the help! Now I am trying to find a high resolution MR DICOM of a head that I can 3D print and use as my phantom. I have been trying to export and use the OsiriX sample data, but when I open it in 3D Slicer most of the scan is missing (it looks cut). Do you know why this might be? I have been searching for sample DICOMs on the web, but nothing I have found so far is high enough resolution for volume rendering, or is in a file format I am not familiar with. 

Thanks and best regards,

Barrett

--
Barrett Anderies
Ambassador | College of Liberal Arts and Sciences
B.S.E. Biomedical Engineering | B.S. Mathematics
Barrett, the Honors College | Arizona State University
Phone: 480-721-9370
           [hidden email]

On Thu, Feb 16, 2017 at 10:28 AM, Andras Lasso <[hidden email]> wrote:

You can use any DICOM data, no need to have fiducial markers in the image. You can either do landmark registration or surface registration, both supported by SlicerIGT extension.

 

Landmark registration is simple, fast, and robust, so we use that for patient registration most of the time. You can either use anatomical landmarks (points that you can identify in the image and on the surface of the 3D-printed phantom) or draw a few divots in the segment editor.

 

For surface registration, you can collect points using Collect fiducials module and register using Fiducials-model registration module. Fiducials-model registration module requires a good initial guess, you can get that from either manual alignment or landmark registration.

 

See SlicerIGT tutorials for step-by-step instructions:

http://www.slicerigt.org/wp/user-tutorial/

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: February 16, 2017 11:47
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Phantom for SlicerIGT regisration

 

Hello all,

 

I am trying to use Slicer with a Polaris Vicra optical tracking camera through the SlicerIGTI extension for my senior engineering project. I am a new to Slicer, and am still trying to learn its features. I have managed to configure my PLUS Server to send the appropriate data to the SlicerIGT OpenIGTLink client, and have visualized tool positions in the 3D view of Slicer. However, I am now faced with registering a phantom for testing. I was hoping to get some advice about the best way to do this. I am operating on a small budget, so I might not be able to get an MRI scan of something with fiducial markers. However, I do have access to a high end 3D printer, so if I could obtain a DICOM of any object with fiducial, I could 3D print a full scale mode of this DICOM. This video shows an example of what I am trying to do: https://www.youtube.com/watch?v=R3ROA94bbOg. Does anyone in the Slicer community have a DICOM of an object or patient (anonymized) with fiducials that they would be willing to share with me? Does anyone have any suggestion? As far as I understand, SlicerIGT only supports fiducial registration. If I could find a way to use a registration method that allows tracing of anatomy with a stylus to collect points, I could use any DICOM from my lab. Does SlicerIGT support anatomy-based registration (like that used by the Medtronic StealthStation)?

 

Thanks and best regards,

 

Barrett


--

Barrett Anderies

B.S.E. Biomedical Engineering | B.S. Mathematics

Barrett, the Honors College | Arizona State University

Phone: <a href="tel:(480)%20721-9370" value="&#43;14807219370" target="_blank"> 480-721-9370

           [hidden email]



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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Phantom for SlicerIGT regisration

barrett.anderies@asu.edu
In reply to this post by Andras Lasso-2
Hi Tamas,

Thank you! It sounds as if landmark or surface registration will be the better option for me. I have found the related tutorials and will refer to them.

Thanks,

Barrett

--
Barrett Anderies
Ambassador | College of Liberal Arts and Sciences
B.S.E. Biomedical Engineering | B.S. Mathematics
Barrett, the Honors College | Arizona State University
Phone: 480-721-9370
           [hidden email]

On Thu, Feb 16, 2017 at 1:12 PM, Tamas Ungi <[hidden email]> wrote:

I think you could use any natural corner point as a fiducial. If you look at the landmark registration and surface registration tutorials at the slicerigt website you will see that those models don't have fiducials either.

Sent from my phone



From: slicer-users <[hidden email]> on behalf of Andras Lasso <[hidden email]>
Sent: Thursday, February 16, 2017 12:28:17 PM
To: [hidden email]; SPL Slicer Users
Subject: Re: [slicer-users] Phantom for SlicerIGT regisration
 

You can use any DICOM data, no need to have fiducial markers in the image. You can either do landmark registration or surface registration, both supported by SlicerIGT extension.

 

Landmark registration is simple, fast, and robust, so we use that for patient registration most of the time. You can either use anatomical landmarks (points that you can identify in the image and on the surface of the 3D-printed phantom) or draw a few divots in the segment editor.

 

For surface registration, you can collect points using Collect fiducials module and register using Fiducials-model registration module. Fiducials-model registration module requires a good initial guess, you can get that from either manual alignment or landmark registration.

 

See SlicerIGT tutorials for step-by-step instructions:

http://www.slicerigt.org/wp/user-tutorial/

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: February 16, 2017 11:47
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Phantom for SlicerIGT regisration

 

Hello all,

 

I am trying to use Slicer with a Polaris Vicra optical tracking camera through the SlicerIGTI extension for my senior engineering project. I am a new to Slicer, and am still trying to learn its features. I have managed to configure my PLUS Server to send the appropriate data to the SlicerIGT OpenIGTLink client, and have visualized tool positions in the 3D view of Slicer. However, I am now faced with registering a phantom for testing. I was hoping to get some advice about the best way to do this. I am operating on a small budget, so I might not be able to get an MRI scan of something with fiducial markers. However, I do have access to a high end 3D printer, so if I could obtain a DICOM of any object with fiducial, I could 3D print a full scale mode of this DICOM. This video shows an example of what I am trying to do: https://www.youtube.com/watch?v=R3ROA94bbOg. Does anyone in the Slicer community have a DICOM of an object or patient (anonymized) with fiducials that they would be willing to share with me? Does anyone have any suggestion? As far as I understand, SlicerIGT only supports fiducial registration. If I could find a way to use a registration method that allows tracing of anatomy with a stylus to collect points, I could use any DICOM from my lab. Does SlicerIGT support anatomy-based registration (like that used by the Medtronic StealthStation)?

 

Thanks and best regards,

 

Barrett


--

Barrett Anderies

B.S.E. Biomedical Engineering | B.S. Mathematics

Barrett, the Honors College | Arizona State University

Phone: <a href="tel:(480)%20721-9370" value="&#43;14807219370" target="_blank"> 480-721-9370

           [hidden email]



_______________________________________________
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