Add fiducial to hierarchy

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

Add fiducial to hierarchy

Zheng Liu

Hello all,

 

I am new slicer user and have a problem. In the annotation module, I placed the fiducial point in the image. However it is not added to any hierarchy (it looks different in a training movie). They  can be found in the markup module. How to add it to a hierarchy?

 

Thanks for your reply.

 

Zheng Liu, PhD

Research Associate

Advanced Imaging Research Center

Oregon National Primate Research Center

Oregon Health & Science University

Portland, OR  97239

Phone:  (503)614-3755

 


_______________________________________________
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


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.
Reply | Threaded
Open this post in threaded view
|

Re: Add fiducial to hierarchy

Tamas Ungi-2

Hi Zheng,

 

Fiducials have been moved to the Markups module. I think you are not supposed to (cannot) create fiducials as annotations anymore. The Markups module creates a list of fiducials automatically as you place a fiducial on an image. That list (by default the name is "F") is in the transform hierarchy, it shows up in the Data module.

 

Hope this helps,

Tamas

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Zheng Liu
Sent: November 4, 2014 9:15 PM
To: [hidden email]
Subject: [slicer-users] Add fiducial to hierarchy

 

Hello all,

 

I am new slicer user and have a problem. In the annotation module, I placed the fiducial point in the image. However it is not added to any hierarchy (it looks different in a training movie). They  can be found in the markup module. How to add it to a hierarchy?

 

Thanks for your reply.

 

Zheng Liu, PhD

Research Associate

Advanced Imaging Research Center

Oregon National Primate Research Center

Oregon Health & Science University

Portland, OR  97239

Phone:  (503)614-3755

 


_______________________________________________
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


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.
Reply | Threaded
Open this post in threaded view
|

Re: Add fiducial to hierarchy

Zheng Liu

Hi all,

 

Is there manual about ACPC transform module? I place two fiducials under “ACPC Line” and five under “Midline”. Then “Apply” (means run???) and “SAVE” the results to a chosen file.

However, when I opened the saved .nii.gz file, it seems no change.

Is the procedure correct?

 

Thanks,

Zheng

 

From: Tamas Ungi [mailto:[hidden email]]
Sent: Tuesday, November 04, 2014 7:17 PM
To: Zheng Liu; [hidden email]
Subject: RE: Add fiducial to hierarchy

 

Hi Zheng,

 

Fiducials have been moved to the Markups module. I think you are not supposed to (cannot) create fiducials as annotations anymore. The Markups module creates a list of fiducials automatically as you place a fiducial on an image. That list (by default the name is "F") is in the transform hierarchy, it shows up in the Data module.

 

Hope this helps,

Tamas

 

 

From: [hidden email] [[hidden email]] On Behalf Of Zheng Liu
Sent: November 4, 2014 9:15 PM
To: [hidden email]
Subject: [slicer-users] Add fiducial to hierarchy

 

Hello all,

 

I am new slicer user and have a problem. In the annotation module, I placed the fiducial point in the image. However it is not added to any hierarchy (it looks different in a training movie). They  can be found in the markup module. How to add it to a hierarchy?

 

Thanks for your reply.

 

Zheng Liu, PhD

Research Associate

Advanced Imaging Research Center

Oregon National Primate Research Center

Oregon Health & Science University

Portland, OR  97239

Phone:  (503)614-3755

 


_______________________________________________
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


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.
Reply | Threaded
Open this post in threaded view
|

Re: Add fiducial to hierarchy

Aucoin, Nicole
Hi Zheng,

There's the module manual page, it mentions that you need to use a
resampling module to apply the transform after creating it:
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/ACPCTransform

Nicole

On 11/5/14 12:47 PM, Zheng Liu wrote:

>
> Hi all,
>
> Is there manual about ACPC transform module? I place two fiducials
> under “ACPC Line” and five under “Midline”. Then “Apply” (means
> run???) and “SAVE” the results to a chosen file.
>
> However, when I opened the saved .nii.gz file, it seems no change.
>
> Is the procedure correct?
>
> Thanks,
>
> Zheng
>
> *From:*Tamas Ungi [mailto:[hidden email]]
> *Sent:* Tuesday, November 04, 2014 7:17 PM
> *To:* Zheng Liu; [hidden email]
> *Subject:* RE: Add fiducial to hierarchy
>
> Hi Zheng,
>
> Fiducials have been moved to the Markups module. I think you are not
> supposed to (cannot) create fiducials as annotations anymore. The
> Markups module creates a list of fiducials automatically as you place
> a fiducial on an image. That list (by default the name is "F") is in
> the transform hierarchy, it shows up in the Data module.
>
> Hope this helps,
>
> Tamas
>
> *From:* [hidden email]
> <mailto:[hidden email]>
> [mailto:[hidden email]] *On Behalf Of *Zheng Liu
> *Sent:* November 4, 2014 9:15 PM
> *To:* [hidden email] <mailto:[hidden email]>
> *Subject:* [slicer-users] Add fiducial to hierarchy
>
> Hello all,
>
> I am new slicer user and have a problem. In the annotation module, I
> placed the fiducial point in the image. However it is not added to any
> hierarchy (it looks different in a training movie). They can be found
> in the markup module. How to add it to a hierarchy?
>
> Thanks for your reply.
>
> Zheng Liu, PhD
>
> Research Associate
>
> Advanced Imaging Research Center
>
> Oregon National Primate Research Center
>
> Oregon Health & Science University
>
> Portland, OR 97239
>
> Phone: (503)614-3755
>
>
>
> _______________________________________________
> 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

_______________________________________________
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


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.

Reply | Threaded
Open this post in threaded view
|

Re: Add fiducial to hierarchy

Zheng Liu
In reply to this post by Tamas Ungi-2

Hello all,

 

I used “ACPC transform” and “Resample Scalar/Vector/DWI Volume” to implement ac-pc alignment. The result in the Slicer seems good. But when save as *.nii file and opened it with ITK-snap, it is rotated in the sigittal view. Do you happen to meet the same problem? And how to fix it?

 

Thanks,

Zheng

 

From: Tamas Ungi [mailto:[hidden email]]
Sent: Tuesday, November 04, 2014 7:17 PM
To: Zheng Liu; [hidden email]
Subject: RE: Add fiducial to hierarchy

 

Hi Zheng,

 

Fiducials have been moved to the Markups module. I think you are not supposed to (cannot) create fiducials as annotations anymore. The Markups module creates a list of fiducials automatically as you place a fiducial on an image. That list (by default the name is "F") is in the transform hierarchy, it shows up in the Data module.

 

Hope this helps,

Tamas

 

 

From: [hidden email] [[hidden email]] On Behalf Of Zheng Liu
Sent: November 4, 2014 9:15 PM
To: [hidden email]
Subject: [slicer-users] Add fiducial to hierarchy

 

Hello all,

 

I am new slicer user and have a problem. In the annotation module, I placed the fiducial point in the image. However it is not added to any hierarchy (it looks different in a training movie). They  can be found in the markup module. How to add it to a hierarchy?

 

Thanks for your reply.

 

Zheng Liu, PhD

Research Associate

Advanced Imaging Research Center

Oregon National Primate Research Center

Oregon Health & Science University

Portland, OR  97239

Phone:  (503)614-3755

 


_______________________________________________
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


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.