Trouble with Cone beam CT model making

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Trouble with Cone beam CT model making

Gagnon, Greg

Hi, I was wondering if there is an  easy way to deal with a CBCT.  I don’t know if it’s normal but it looks as though the axial window looks like a normal CT but the coronal and sagittal look stretched and upside down.  Everything I’ve read so far about different modules either don’t seem to exist like the Plastimatch or doing some sort of Transform does all three views.  We are trying to view and print the 3d model of the mandible for possible implant planning.  The disk doesn’t seem to have the raw dicom data like most disks I’m used to receiving, I have to just take the entire folder and put it into Slicer.  Do you think that I need to try and get the raw data?  Or if there is any other free software out there that would make easy work of this please advise.  Any help is greatly appreciated. 

 

Thanks,
Greg

 


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Re: Trouble with Cone beam CT model making

Andras Lasso-2

Most probably the CBCT device does not save the result into valid DICOM images. You can go to Volumes module and in the Volume information section enter the correct image spacing information. You might be able to guess the correct value or it may be displayed in the image viewer that is on the CD.

 

To adjust image orientation, go to Transforms module, create a new linear transform, change 1.0 in the diagonal of the Transform Matrix to -1.0 for all axes that you would like to mirror, and apply the transform to the volume.

 

If you often get such corrupted images then it may worth to have a look at the DICOM header to see what’s wrong and fix that (we could add a rule to DICOM Patcher module that fixes common problems in DICOM files).

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Gagnon, Greg
Sent: March 13, 2017 9:16
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Trouble with Cone beam CT model making

 

Hi, I was wondering if there is an  easy way to deal with a CBCT.  I don’t know if it’s normal but it looks as though the axial window looks like a normal CT but the coronal and sagittal look stretched and upside down.  Everything I’ve read so far about different modules either don’t seem to exist like the Plastimatch or doing some sort of Transform does all three views.  We are trying to view and print the 3d model of the mandible for possible implant planning.  The disk doesn’t seem to have the raw dicom data like most disks I’m used to receiving, I have to just take the entire folder and put it into Slicer.  Do you think that I need to try and get the raw data?  Or if there is any other free software out there that would make easy work of this please advise.  Any help is greatly appreciated. 

 

Thanks,
Greg

 


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 with Cone beam CT model making

Sharp, Gregory C.
In reply to this post by Gagnon, Greg

It looks like your slice spacing is not set correctly. 

Try this:

 

è Volumes module

è Volume Information

è Image Spacing

è Edit Z value (the third one), decrease by a factor of 3

 

Does it look better?

 

Many CBCT are isotropic (same spacing in x, y, and z). 

If your X and Y spacing are the same, but Z is different,

try making Z the same as X and Y.

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:16 AM
To: SPL Slicer Users
Subject: [slicer-users] Trouble with Cone beam CT model making

 

Hi, I was wondering if there is an  easy way to deal with a CBCT.  I don’t know if it’s normal but it looks as though the axial window looks like a normal CT but the coronal and sagittal look stretched and upside down.  Everything I’ve read so far about different modules either don’t seem to exist like the Plastimatch or doing some sort of Transform does all three views.  We are trying to view and print the 3d model of the mandible for possible implant planning.  The disk doesn’t seem to have the raw dicom data like most disks I’m used to receiving, I have to just take the entire folder and put it into Slicer.  Do you think that I need to try and get the raw data?  Or if there is any other free software out there that would make easy work of this please advise.  Any help is greatly appreciated. 

 

Thanks,
Greg

 


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 with Cone beam CT model making

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

Mr. Sharp.  You NAILED it haha.  Thank you so much.  I can’t believe I spent two days trying to figure that out and it was so simple.  Like anything else every day I learn something new.  Today is no different!  Thanks to everyone

 

From: Sharp, Gregory C. [mailto:[hidden email]]
Sent: Monday, March 13, 2017 9:39 AM
To: Gagnon, Greg; SPL Slicer Users
Subject: RE: Trouble with Cone beam CT model making

 

It looks like your slice spacing is not set correctly. 

Try this:

 

è Volumes module

è Volume Information

è Image Spacing

è Edit Z value (the third one), decrease by a factor of 3

 

Does it look better?

 

Many CBCT are isotropic (same spacing in x, y, and z). 

If your X and Y spacing are the same, but Z is different,

try making Z the same as X and Y.

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:16 AM
To: SPL Slicer Users
Subject: [slicer-users] Trouble with Cone beam CT model making

 

Hi, I was wondering if there is an  easy way to deal with a CBCT.  I don’t know if it’s normal but it looks as though the axial window looks like a normal CT but the coronal and sagittal look stretched and upside down.  Everything I’ve read so far about different modules either don’t seem to exist like the Plastimatch or doing some sort of Transform does all three views.  We are trying to view and print the 3d model of the mandible for possible implant planning.  The disk doesn’t seem to have the raw dicom data like most disks I’m used to receiving, I have to just take the entire folder and put it into Slicer.  Do you think that I need to try and get the raw data?  Or if there is any other free software out there that would make easy work of this please advise.  Any help is greatly appreciated. 

 

Thanks,
Greg

 


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.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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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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Re: Trouble with Cone beam CT model making

Sharp, Gregory C.

Glad to help.  If you are doing quantitative analysis, please contact the data provider or manufacturer.  Maybe (x,y) spacing or other image parameters are incorrect too.  -Greg

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:48 AM
To: Sharp, Gregory C.; SPL Slicer Users
Subject: Re: [slicer-users] Trouble with Cone beam CT model making

 

Mr. Sharp.  You NAILED it haha.  Thank you so much.  I can’t believe I spent two days trying to figure that out and it was so simple.  Like anything else every day I learn something new.  Today is no different!  Thanks to everyone

 

From: Sharp, Gregory C. [[hidden email]]
Sent: Monday, March 13, 2017 9:39 AM
To: Gagnon, Greg; SPL Slicer Users
Subject: RE: Trouble with Cone beam CT model making

 

It looks like your slice spacing is not set correctly. 

Try this:

 

è Volumes module

è Volume Information

è Image Spacing

è Edit Z value (the third one), decrease by a factor of 3

 

Does it look better?

 

Many CBCT are isotropic (same spacing in x, y, and z). 

If your X and Y spacing are the same, but Z is different,

try making Z the same as X and Y.

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:16 AM
To: SPL Slicer Users
Subject: [slicer-users] Trouble with Cone beam CT model making

 

Hi, I was wondering if there is an  easy way to deal with a CBCT.  I don’t know if it’s normal but it looks as though the axial window looks like a normal CT but the coronal and sagittal look stretched and upside down.  Everything I’ve read so far about different modules either don’t seem to exist like the Plastimatch or doing some sort of Transform does all three views.  We are trying to view and print the 3d model of the mandible for possible implant planning.  The disk doesn’t seem to have the raw dicom data like most disks I’m used to receiving, I have to just take the entire folder and put it into Slicer.  Do you think that I need to try and get the raw data?  Or if there is any other free software out there that would make easy work of this please advise.  Any help is greatly appreciated. 

 

Thanks,
Greg

 


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.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: Trouble with Cone beam CT model making

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

Well I thought I had everything correct.  The image is the correct size and shape but it is a mirror image of what it’s supposed to be.  I tried doing the -1.0 diagonal in the transforms screen but nothing happened.  Am I missing something simple again?  I can always just mirror it in Meshmixer but I figured if it’s simple in Slicer I might as well do it ahead of time.

 

Thanks again,

Greg

 

From: Sharp, Gregory C. [mailto:[hidden email]]
Sent: Monday, March 13, 2017 11:37 AM
To: Gagnon, Greg; SPL Slicer Users
Subject: RE: Trouble with Cone beam CT model making

 

Glad to help.  If you are doing quantitative analysis, please contact the data provider or manufacturer.  Maybe (x,y) spacing or other image parameters are incorrect too.  -Greg

 

From: slicer-users [hidden email] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:48 AM
To: Sharp, Gregory C.; SPL Slicer Users
Subject: Re: [slicer-users] Trouble with Cone beam CT model making

 

Mr. Sharp.  You NAILED it haha.  Thank you so much.  I can’t believe I spent two days trying to figure that out and it was so simple.  Like anything else every day I learn something new.  Today is no different!  Thanks to everyone

 

From: Sharp, Gregory C. [[hidden email]]
Sent: Monday, March 13, 2017 9:39 AM
To: Gagnon, Greg; SPL Slicer Users
Subject: RE: Trouble with Cone beam CT model making

 

It looks like your slice spacing is not set correctly. 

Try this:

 

è Volumes module

è Volume Information

è Image Spacing

è Edit Z value (the third one), decrease by a factor of 3

 

Does it look better?

 

Many CBCT are isotropic (same spacing in x, y, and z). 

If your X and Y spacing are the same, but Z is different,

try making Z the same as X and Y.

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:16 AM
To: SPL Slicer Users
Subject: [slicer-users] Trouble with Cone beam CT model making

 

Hi, I was wondering if there is an  easy way to deal with a CBCT.  I don’t know if it’s normal but it looks as though the axial window looks like a normal CT but the coronal and sagittal look stretched and upside down.  Everything I’ve read so far about different modules either don’t seem to exist like the Plastimatch or doing some sort of Transform does all three views.  We are trying to view and print the 3d model of the mandible for possible implant planning.  The disk doesn’t seem to have the raw dicom data like most disks I’m used to receiving, I have to just take the entire folder and put it into Slicer.  Do you think that I need to try and get the raw data?  Or if there is any other free software out there that would make easy work of this please advise.  Any help is greatly appreciated. 

 

Thanks,
Greg

 


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.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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 with Cone beam CT model making

Andras Lasso-2

Make sure to apply the transform to the nodes that you want to mirror (nodes should be listed on the right side in the Transforms module’s Apply section).

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 14, 2017 4:30 PM
To: [hidden email]; [hidden email]
Subject: Re: [slicer-users] Trouble with Cone beam CT model making

 

Well I thought I had everything correct.  The image is the correct size and shape but it is a mirror image of what it’s supposed to be.  I tried doing the -1.0 diagonal in the transforms screen but nothing happened.  Am I missing something simple again?  I can always just mirror it in Meshmixer but I figured if it’s simple in Slicer I might as well do it ahead of time.

 

Thanks again,

Greg

 

From: Sharp, Gregory C. [mailto:[hidden email]]
Sent: Monday, March 13, 2017 11:37 AM
To: Gagnon, Greg; SPL Slicer Users
Subject: RE: Trouble with Cone beam CT model making

 

Glad to help.  If you are doing quantitative analysis, please contact the data provider or manufacturer.  Maybe (x,y) spacing or other image parameters are incorrect too.  -Greg

 

From: slicer-users [hidden email] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:48 AM
To: Sharp, Gregory C.; SPL Slicer Users
Subject: Re: [slicer-users] Trouble with Cone beam CT model making

 

Mr. Sharp.  You NAILED it haha.  Thank you so much.  I can’t believe I spent two days trying to figure that out and it was so simple.  Like anything else every day I learn something new.  Today is no different!  Thanks to everyone

 

From: Sharp, Gregory C. [[hidden email]]
Sent: Monday, March 13, 2017 9:39 AM
To: Gagnon, Greg; SPL Slicer Users
Subject: RE: Trouble with Cone beam CT model making

 

It looks like your slice spacing is not set correctly. 

Try this:

 

è Volumes module

è Volume Information

è Image Spacing

è Edit Z value (the third one), decrease by a factor of 3

 

Does it look better?

 

Many CBCT are isotropic (same spacing in x, y, and z). 

If your X and Y spacing are the same, but Z is different,

try making Z the same as X and Y.

 

From: slicer-users [[hidden email]] On Behalf Of Gagnon, Greg
Sent: Monday, March 13, 2017 9:16 AM
To: SPL Slicer Users
Subject: [slicer-users] Trouble with Cone beam CT model making

 

Hi, I was wondering if there is an  easy way to deal with a CBCT.  I don’t know if it’s normal but it looks as though the axial window looks like a normal CT but the coronal and sagittal look stretched and upside down.  Everything I’ve read so far about different modules either don’t seem to exist like the Plastimatch or doing some sort of Transform does all three views.  We are trying to view and print the 3d model of the mandible for possible implant planning.  The disk doesn’t seem to have the raw dicom data like most disks I’m used to receiving, I have to just take the entire folder and put it into Slicer.  Do you think that I need to try and get the raw data?  Or if there is any other free software out there that would make easy work of this please advise.  Any help is greatly appreciated. 

 

Thanks,
Greg

 


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.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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.

_______________________________________________
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