Trouble aligning MRI and CT data in same model

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Trouble aligning MRI and CT data in same model

Gagnon, Greg

                Hi, this is Greg Gagnon from Clinical Engineering at Baystate Medical Center in Springfield, MA.  When I went to the contact-us section in the Slicerwiki I was surprised to see the email address.  I had no idea that BWH and Harvard had so much to do with 3DSlicer.  Over the last couple years I’ve made quite a few models at our hospital for patient education and pre-surgical planning using all sorts of various open source software.  I’ve decided that 3Dslicer is probably my best bet once I learn it inside and out until we can afford something like Materialise.  So my current problem is matching up MRI scans (for locating tumors) and CT scans (for segmenting out the bone structures) to make models for our cancer center.  I can usually make a model reasonably close by comparing the scans and manually moving the objects but I want to take the guess work out of it.  In Slicer I was successful once with loading the two separate volumes (one MRI and one CT) and creating the objects to where they showed up in the 3d rendering correctly.  Once I exported them into meshmixer the tumor was about ten times larger than it was supposed to be and not in the correct location.  After hours and days of trying different things now I can’t even get them to show up in Slicer in the correct position.  I’ve been in contact and visited Dr. Prabhu at Boston Children’s and he did mention that you may know best as to how to get this corrected.  I feel as though I’m pretty comfortable with the basics of using the software and have gone through hours and hours of tutorials.  Is there anyone in the MA area that would be willing to let me do a site visit and go over how to correct this issue?  Also if there is a particular tutorial on aligning separate volumes that would be great too.  Any help is appreciated!

 

Thanks,
Greg Gagnon

Clinical Engineering

Baystate Medical Center

Springfield, MA 01199


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at https://www.baystatehealth.org.

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Re: Trouble aligning MRI and CT data in same model

Murat Maga

There is an ongoing workshop right now. https://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week. In fact the response is likely to be slow to due to the number of people attending the workshop.

 

What you describe sounds like your volumes lack the proper image spacing and orientation (or at least they are not presented in a way slicer understands it). Trying well supported formats like nifti or nrrd may help.  Cross referencing image dimension values reported in the volumes module to your original data may give you a hint about what the problem is.

 

There is co-registration framework built into Slicer (General Registration module). If the CT and MR comes from the same patient, a rigid registration (after getting rid of your initial problem about sizes and spacing) should help you with what you want to accomplish.

https://www.slicer.org/wiki/Documentation/Nightly/Modules/BRAINSFit

 

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Gagnon, Greg
Sent: Thursday, January 12, 2017 10:02 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Trouble aligning MRI and CT data in same model

 

                Hi, this is Greg Gagnon from Clinical Engineering at Baystate Medical Center in Springfield, MA.  When I went to the contact-us section in the Slicerwiki I was surprised to see the email address.  I had no idea that BWH and Harvard had so much to do with 3DSlicer.  Over the last couple years I’ve made quite a few models at our hospital for patient education and pre-surgical planning using all sorts of various open source software.  I’ve decided that 3Dslicer is probably my best bet once I learn it inside and out until we can afford something like Materialise.  So my current problem is matching up MRI scans (for locating tumors) and CT scans (for segmenting out the bone structures) to make models for our cancer center.  I can usually make a model reasonably close by comparing the scans and manually moving the objects but I want to take the guess work out of it.  In Slicer I was successful once with loading the two separate volumes (one MRI and one CT) and creating the objects to where they showed up in the 3d rendering correctly.  Once I exported them into meshmixer the tumor was about ten times larger than it was supposed to be and not in the correct location.  After hours and days of trying different things now I can’t even get them to show up in Slicer in the correct position.  I’ve been in contact and visited Dr. Prabhu at Boston Children’s and he did mention that you may know best as to how to get this corrected.  I feel as though I’m pretty comfortable with the basics of using the software and have gone through hours and hours of tutorials.  Is there anyone in the MA area that would be willing to let me do a site visit and go over how to correct this issue?  Also if there is a particular tutorial on aligning separate volumes that would be great too.  Any help is appreciated!

 

Thanks,
Greg Gagnon

Clinical Engineering

Baystate Medical Center

Springfield, MA 01199


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at
https://www.baystatehealth.org.


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Re: Trouble aligning MRI and CT data in same model

Gagnon, Greg
In reply to this post by Gagnon, Greg

Yes, sorry I forgot to mention I did get an error that said geometry of master and merge volumes do not match.  So I tried messing with the Image Origin and the Image Spacing in the Volumes module but nothing seemed to help.

 

From: Murat Maga [mailto:[hidden email]]
Sent: Thursday, January 12, 2017 1:23 PM
To: Gagnon, Greg
Cc: SPL Slicer Users
Subject: RE: Trouble aligning MRI and CT data in same model

 

There is an ongoing workshop right now. https://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week. In fact the response is likely to be slow to due to the number of people attending the workshop.

 

What you describe sounds like your volumes lack the proper image spacing and orientation (or at least they are not presented in a way slicer understands it). Trying well supported formats like nifti or nrrd may help.  Cross referencing image dimension values reported in the volumes module to your original data may give you a hint about what the problem is.

 

There is co-registration framework built into Slicer (General Registration module). If the CT and MR comes from the same patient, a rigid registration (after getting rid of your initial problem about sizes and spacing) should help you with what you want to accomplish.

https://www.slicer.org/wiki/Documentation/Nightly/Modules/BRAINSFit

 

 

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Thursday, January 12, 2017 10:02 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Trouble aligning MRI and CT data in same model

 

                Hi, this is Greg Gagnon from Clinical Engineering at Baystate Medical Center in Springfield, MA.  When I went to the contact-us section in the Slicerwiki I was surprised to see the email address.  I had no idea that BWH and Harvard had so much to do with 3DSlicer.  Over the last couple years I’ve made quite a few models at our hospital for patient education and pre-surgical planning using all sorts of various open source software.  I’ve decided that 3Dslicer is probably my best bet once I learn it inside and out until we can afford something like Materialise.  So my current problem is matching up MRI scans (for locating tumors) and CT scans (for segmenting out the bone structures) to make models for our cancer center.  I can usually make a model reasonably close by comparing the scans and manually moving the objects but I want to take the guess work out of it.  In Slicer I was successful once with loading the two separate volumes (one MRI and one CT) and creating the objects to where they showed up in the 3d rendering correctly.  Once I exported them into meshmixer the tumor was about ten times larger than it was supposed to be and not in the correct location.  After hours and days of trying different things now I can’t even get them to show up in Slicer in the correct position.  I’ve been in contact and visited Dr. Prabhu at Boston Children’s and he did mention that you may know best as to how to get this corrected.  I feel as though I’m pretty comfortable with the basics of using the software and have gone through hours and hours of tutorials.  Is there anyone in the MA area that would be willing to let me do a site visit and go over how to correct this issue?  Also if there is a particular tutorial on aligning separate volumes that would be great too.  Any help is appreciated!

 

Thanks,
Greg Gagnon

Clinical Engineering

Baystate Medical Center

Springfield, MA 01199


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at
https://www.baystatehealth.org.


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at https://www.baystatehealth.org.

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Re: Trouble aligning MRI and CT data in same model

Kikinis, Ron,M.D.
In reply to this post by Murat Maga
Hi,

in addition, you might want to look at the registration library, which provides examples scenarios and solutions.

https://www.slicer.org/wiki/Documentation/Nightly/Registration/RegistrationLibrary

Ron

> On Jan 12, 2017, at 1:22 PM, Murat Maga <[hidden email]> wrote:
>
> There is an ongoing workshop right now. https://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week. In fact the response is likely to be slow to due to the number of people attending the workshop.
>  
> What you describe sounds like your volumes lack the proper image spacing and orientation (or at least they are not presented in a way slicer understands it). Trying well supported formats like nifti or nrrd may help.  Cross referencing image dimension values reported in the volumes module to your original data may give you a hint about what the problem is.
>  
> There is co-registration framework built into Slicer (General Registration module). If the CT and MR comes from the same patient, a rigid registration (after getting rid of your initial problem about sizes and spacing) should help you with what you want to accomplish.
> https://www.slicer.org/wiki/Documentation/Nightly/Modules/BRAINSFit
>  
>  
>  
> From: slicer-users [mailto:[hidden email]] On Behalf Of Gagnon, Greg
> Sent: Thursday, January 12, 2017 10:02 AM
> To: SPL Slicer Users <[hidden email]>
> Subject: [slicer-users] Trouble aligning MRI and CT data in same model
>  
>                 Hi, this is Greg Gagnon from Clinical Engineering at Baystate Medical Center in Springfield, MA.  When I went to the contact-us section in the Slicerwiki I was surprised to see the email address.  I had no idea that BWH and Harvard had so much to do with 3DSlicer.  Over the last couple years I’ve made quite a few models at our hospital for patient education and pre-surgical planning using all sorts of various open source software.  I’ve decided that 3Dslicer is probably my best bet once I learn it inside and out until we can afford something like Materialise.  So my current problem is matching up MRI scans (for locating tumors) and CT scans (for segmenting out the bone structures) to make models for our cancer center.  I can usually make a model reasonably close by comparing the scans and manually moving the objects but I want to take the guess work out of it.  In Slicer I was successful once with loading the two separate volumes (one MRI and one CT) and creating the objects to where they showed up in the 3d rendering correctly.  Once I exported them into meshmixer the tumor was about ten times larger than it was supposed to be and not in the correct location.  After hours and days of trying different things now I can’t even get them to show up in Slicer in the correct position.  I’ve been in contact and visited Dr. Prabhu at Boston Children’s and he did mention that you may know best as to how to get this corrected.  I feel as though I’m pretty comfortable with the basics of using the software and have gone through hours and hours of tutorials.  Is there anyone in the MA area that would be willing to let me do a site visit and go over how to correct this issue?  Also if there is a particular tutorial on aligning separate volumes that would be great too.  Any help is appreciated!
>  
> Thanks,
> Greg Gagnon
> Clinical Engineering
> Baystate Medical Center
> Springfield, MA 01199
> Please view our annual report at http://www.bhannualreport.org
>
>
> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site athttps://www.baystatehealth.org.
> _______________________________________________
> 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

--
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: Trouble aligning MRI and CT data in same model

Andras Lasso-2
In reply to this post by Gagnon, Greg

Instead of “Editor” modules use the new “Segment editor” module (and make sure you use a recent nightly build of Slicer). Segment editor can work on different volumes, so you will not have the “geometry of master and merge volumes do not match“ error.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Gagnon, Greg
Sent: January 12, 2017 13:42
To: Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Trouble aligning MRI and CT data in same model

 

Yes, sorry I forgot to mention I did get an error that said geometry of master and merge volumes do not match.  So I tried messing with the Image Origin and the Image Spacing in the Volumes module but nothing seemed to help.

 

From: Murat Maga [[hidden email]]
Sent: Thursday, January 12, 2017 1:23 PM
To: Gagnon, Greg
Cc: SPL Slicer Users
Subject: RE: Trouble aligning MRI and CT data in same model

 

There is an ongoing workshop right now. https://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week. In fact the response is likely to be slow to due to the number of people attending the workshop.

 

What you describe sounds like your volumes lack the proper image spacing and orientation (or at least they are not presented in a way slicer understands it). Trying well supported formats like nifti or nrrd may help.  Cross referencing image dimension values reported in the volumes module to your original data may give you a hint about what the problem is.

 

There is co-registration framework built into Slicer (General Registration module). If the CT and MR comes from the same patient, a rigid registration (after getting rid of your initial problem about sizes and spacing) should help you with what you want to accomplish.

https://www.slicer.org/wiki/Documentation/Nightly/Modules/BRAINSFit

 

 

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Thursday, January 12, 2017 10:02 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Trouble aligning MRI and CT data in same model

 

                Hi, this is Greg Gagnon from Clinical Engineering at Baystate Medical Center in Springfield, MA.  When I went to the contact-us section in the Slicerwiki I was surprised to see the email address.  I had no idea that BWH and Harvard had so much to do with 3DSlicer.  Over the last couple years I’ve made quite a few models at our hospital for patient education and pre-surgical planning using all sorts of various open source software.  I’ve decided that 3Dslicer is probably my best bet once I learn it inside and out until we can afford something like Materialise.  So my current problem is matching up MRI scans (for locating tumors) and CT scans (for segmenting out the bone structures) to make models for our cancer center.  I can usually make a model reasonably close by comparing the scans and manually moving the objects but I want to take the guess work out of it.  In Slicer I was successful once with loading the two separate volumes (one MRI and one CT) and creating the objects to where they showed up in the 3d rendering correctly.  Once I exported them into meshmixer the tumor was about ten times larger than it was supposed to be and not in the correct location.  After hours and days of trying different things now I can’t even get them to show up in Slicer in the correct position.  I’ve been in contact and visited Dr. Prabhu at Boston Children’s and he did mention that you may know best as to how to get this corrected.  I feel as though I’m pretty comfortable with the basics of using the software and have gone through hours and hours of tutorials.  Is there anyone in the MA area that would be willing to let me do a site visit and go over how to correct this issue?  Also if there is a particular tutorial on aligning separate volumes that would be great too.  Any help is appreciated!

 

Thanks,
Greg Gagnon

Clinical Engineering

Baystate Medical Center

Springfield, MA 01199


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at
https://www.baystatehealth.org.


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at https://www.baystatehealth.org.


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Re: Trouble aligning MRI and CT data in same model

Dominik Meier-2
In reply to this post by Gagnon, Greg
Hi Greg

This is not an uncommon problem that can arise if there are even very small (roundoff) differences in voxel size etc. May not be apparent from looking at the numbers.
You could try resample the image with one of the Resample modules, with an identity transform and the master volume as a reference. This should not change the image data significantly but as a side effect will match up all the geometry values.

Dominik



On 12 Jan 2017, at 19:41, Gagnon, Greg <[hidden email]> wrote:

Yes, sorry I forgot to mention I did get an error that said geometry of master and merge volumes do not match.  So I tried messing with the Image Origin and the Image Spacing in the Volumes module but nothing seemed to help.

 

From: Murat Maga [[hidden email]]
Sent: Thursday, January 12, 2017 1:23 PM
To: Gagnon, Greg
Cc: SPL Slicer Users
Subject: RE: Trouble aligning MRI and CT data in same model

 

There is an ongoing workshop right now. https://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week. In fact the response is likely to be slow to due to the number of people attending the workshop.

 

What you describe sounds like your volumes lack the proper image spacing and orientation (or at least they are not presented in a way slicer understands it). Trying well supported formats like nifti or nrrd may help.  Cross referencing image dimension values reported in the volumes module to your original data may give you a hint about what the problem is.

 

There is co-registration framework built into Slicer (General Registration module). If the CT and MR comes from the same patient, a rigid registration (after getting rid of your initial problem about sizes and spacing) should help you with what you want to accomplish.

https://www.slicer.org/wiki/Documentation/Nightly/Modules/BRAINSFit

 

 

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Thursday, January 12, 2017 10:02 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Trouble aligning MRI and CT data in same model

 

                Hi, this is Greg Gagnon from Clinical Engineering at Baystate Medical Center in Springfield, MA.  When I went to the contact-us section in the Slicerwiki I was surprised to see the email address.  I had no idea that BWH and Harvard had so much to do with 3DSlicer.  Over the last couple years I’ve made quite a few models at our hospital for patient education and pre-surgical planning using all sorts of various open source software.  I’ve decided that 3Dslicer is probably my best bet once I learn it inside and out until we can afford something like Materialise.  So my current problem is matching up MRI scans (for locating tumors) and CT scans (for segmenting out the bone structures) to make models for our cancer center.  I can usually make a model reasonably close by comparing the scans and manually moving the objects but I want to take the guess work out of it.  In Slicer I was successful once with loading the two separate volumes (one MRI and one CT) and creating the objects to where they showed up in the 3d rendering correctly.  Once I exported them into meshmixer the tumor was about ten times larger than it was supposed to be and not in the correct location.  After hours and days of trying different things now I can’t even get them to show up in Slicer in the correct position.  I’ve been in contact and visited Dr. Prabhu at Boston Children’s and he did mention that you may know best as to how to get this corrected.  I feel as though I’m pretty comfortable with the basics of using the software and have gone through hours and hours of tutorials.  Is there anyone in the MA area that would be willing to let me do a site visit and go over how to correct this issue?  Also if there is a particular tutorial on aligning separate volumes that would be great too.  Any help is appreciated!

 

Thanks,
Greg Gagnon

Clinical Engineering

Baystate Medical Center

Springfield, MA 01199


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at
https://www.baystatehealth.org.


Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at https://www.baystatehealth.org.
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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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Re: Trouble aligning MRI and CT data in same model

Andras Lasso-2
In reply to this post by Gagnon, Greg

There is also a new tutorial that Csaba has created explaining how to use the new Segment editor module.

 

The tutorial shows how to create a 3D-printable model by combining structures segmented from CT image with parts designed in CAD software.

 

http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf

 

(future updates may be available here: http://www.na-mic.org/Wiki/index.php/File:SegmentationFor3DPrinting_TutorialContestWinter2017.pptx)

 

Andras

 

From: Andras Lasso
Sent: January 12, 2017 14:16
To: 'Gagnon, Greg' <[hidden email]>; Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: RE: Trouble aligning MRI and CT data in same model

 

Instead of “Editor” modules use the new “Segment editor” module (and make sure you use a recent nightly build of Slicer). Segment editor can work on different volumes, so you will not have the “geometry of master and merge volumes do not match“ error.

 

Andras

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: January 12, 2017 13:42
To: Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Trouble aligning MRI and CT data in same model

 

Yes, sorry I forgot to mention I did get an error that said geometry of master and merge volumes do not match.  So I tried messing with the Image Origin and the Image Spacing in the Volumes module but nothing seemed to help.

 

From: Murat Maga [[hidden email]]
Sent: Thursday, January 12, 2017 1:23 PM
To: Gagnon, Greg
Cc: SPL Slicer Users
Subject: RE: Trouble aligning MRI and CT data in same model

 

There is an ongoing workshop right now. https://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week. In fact the response is likely to be slow to due to the number of people attending the workshop.

 

What you describe sounds like your volumes lack the proper image spacing and orientation (or at least they are not presented in a way slicer understands it). Trying well supported formats like nifti or nrrd may help.  Cross referencing image dimension values reported in the volumes module to your original data may give you a hint about what the problem is.

 

There is co-registration framework built into Slicer (General Registration module). If the CT and MR comes from the same patient, a rigid registration (after getting rid of your initial problem about sizes and spacing) should help you with what you want to accomplish.

https://www.slicer.org/wiki/Documentation/Nightly/Modules/BRAINSFit

 

 

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Thursday, January 12, 2017 10:02 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Trouble aligning MRI and CT data in same model

 

                Hi, this is Greg Gagnon from Clinical Engineering at Baystate Medical Center in Springfield, MA.  When I went to the contact-us section in the Slicerwiki I was surprised to see the email address.  I had no idea that BWH and Harvard had so much to do with 3DSlicer.  Over the last couple years I’ve made quite a few models at our hospital for patient education and pre-surgical planning using all sorts of various open source software.  I’ve decided that 3Dslicer is probably my best bet once I learn it inside and out until we can afford something like Materialise.  So my current problem is matching up MRI scans (for locating tumors) and CT scans (for segmenting out the bone structures) to make models for our cancer center.  I can usually make a model reasonably close by comparing the scans and manually moving the objects but I want to take the guess work out of it.  In Slicer I was successful once with loading the two separate volumes (one MRI and one CT) and creating the objects to where they showed up in the 3d rendering correctly.  Once I exported them into meshmixer the tumor was about ten times larger than it was supposed to be and not in the correct location.  After hours and days of trying different things now I can’t even get them to show up in Slicer in the correct position.  I’ve been in contact and visited Dr. Prabhu at Boston Children’s and he did mention that you may know best as to how to get this corrected.  I feel as though I’m pretty comfortable with the basics of using the software and have gone through hours and hours of tutorials.  Is there anyone in the MA area that would be willing to let me do a site visit and go over how to correct this issue?  Also if there is a particular tutorial on aligning separate volumes that would be great too.  Any help is appreciated!

 

Thanks,
Greg Gagnon

Clinical Engineering

Baystate Medical Center

Springfield, MA 01199


Please view our annual report at http://www.bhannualreport.org


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Please view our annual report at http://www.bhannualreport.org


CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please reply to the sender immediately or by telephone at 413-794-0000 and destroy all copies of this communication and any attachments. For further information regarding Baystate Health's privacy policy, please visit our Internet site at https://www.baystatehealth.org.


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