How to smooth one structure of label maps?

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How to smooth one structure of label maps?

vansure
Dear Slicer Community,

I am trying to smooth one structure of a label map and then to merge the smoothed structure with all other structures in the same label map.

I tried the Label Map Smoothing Module. It did smooth the structure while changed the colour (or label) of the structure and crashed when I tried to merge this smoothed structure with others.

I tried different versions of Slicer on both Windows and OS X but they all crashed. Any suggestion will be appreciated. Thank you.

Best wishes,
Shawn
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Re: How to smooth one structure of label maps?

Steve Pieper-2
Hi Shawn - 

I just tried that and the issue is that the Label Map Smoothing output is an unsigned char volume.  If you us the Cast filter (in Filters->Arithmetic) and select your per-structure volume as both input and output and cast to short then things should work.

HTH,
-Steve

On Tue, Feb 17, 2015 at 6:43 PM, WANG Shuo <[hidden email]> wrote:
Dear Slicer Community,

I am trying to smooth one structure of a label map and then to merge the smoothed structure with all other structures in the same label map.

I tried the Label Map Smoothing Module. It did smooth the structure while changed the colour (or label) of the structure and crashed when I tried to merge this smoothed structure with others.

I tried different versions of Slicer on both Windows and OS X but they all crashed. Any suggestion will be appreciated. Thank you.

Best wishes,
Shawn
_______________________________________________
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



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Re: How to smooth one structure of label maps?

vansure
Hi Steve,

Thank you for your quick reply. Your solution works perfectly.

Thanks,
Shawn

On 18 Feb 2015, at 00:02, Steve Pieper <[hidden email]> wrote:

Hi Shawn - 

I just tried that and the issue is that the Label Map Smoothing output is an unsigned char volume.  If you us the Cast filter (in Filters->Arithmetic) and select your per-structure volume as both input and output and cast to short then things should work.

HTH,
-Steve

On Tue, Feb 17, 2015 at 6:43 PM, WANG Shuo <[hidden email]> wrote:
Dear Slicer Community,

I am trying to smooth one structure of a label map and then to merge the smoothed structure with all other structures in the same label map.

I tried the Label Map Smoothing Module. It did smooth the structure while changed the colour (or label) of the structure and crashed when I tried to merge this smoothed structure with others.

I tried different versions of Slicer on both Windows and OS X but they all crashed. Any suggestion will be appreciated. Thank you.

Best wishes,
Shawn
_______________________________________________
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Do Not See Extensions

Emily Louise Belleau


Hello Slicer Users,


I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.


I checked the application settings and the extension manager is enabled.


Can anyone tell me what might be the problem?


Thanks,


Emily


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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Do Not See Extensions

Timothy Yeung
I had a similar problem before.
Two potential workarounds that worked sporadically. So you can give it a try.
1) When the Extension manager popsup and keeps loading, right click to select "Go Back", and right again click to select "Go Foward". Repeat until the extensions show up (or give up when you are convinced this doesn't work).
2) Uninstall and re-install slicer

Timothy

>>> Emily Louise Belleau <[hidden email]> 02/24/15 12:26 PM >>>


Hello Slicer Users,


I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.


I checked the application settings and the extension manager is enabled.


Can anyone tell me what might be the problem?


Thanks,


Emily



This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation.
_______________________________________________
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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


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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Re: Do Not See Extensions

Emily Louise Belleau

Hello Slicer Users,


I am still having a problem installing the DTIPrep extension. I have tried all of the steps that Timothy has suggested (thanks Tim).


Any thoughts?


Emily


From: Timothy Yeung <[hidden email]>
Sent: Tuesday, February 24, 2015 11:31 AM
To: [hidden email]; Emily Louise Belleau
Subject: Re: [slicer-users] Do Not See Extensions
 
I had a similar problem before.
Two potential workarounds that worked sporadically. So you can give it a try.
1) When the Extension manager popsup and keeps loading, right click to select "Go Back", and right again click to select "Go Foward". Repeat until the extensions show up (or give up when you are convinced this doesn't work).
2) Uninstall and re-install slicer

Timothy

>>> Emily Louise Belleau <[hidden email]> 02/24/15 12:26 PM >>>


Hello Slicer Users,


I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.


I checked the application settings and the extension manager is enabled.


Can anyone tell me what might be the problem?


Thanks,


Emily



This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation.

_______________________________________________
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[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
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Re: Do Not See Extensions

Carol Johnson
I have been having the same issues.
However, I just tried logging in as an administrator and using Internet Explorer as my browser, I was able to access the appstore with this link http://slicer.kitware.com/midas3/slicerappstore

Hope this helps
Carol

On Tue, Feb 24, 2015 at 2:31 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Users,


I am still having a problem installing the DTIPrep extension. I have tried all of the steps that Timothy has suggested (thanks Tim).


Any thoughts?


Emily


From: Timothy Yeung <[hidden email]>
Sent: Tuesday, February 24, 2015 11:31 AM
To: [hidden email]; Emily Louise Belleau
Subject: Re: [slicer-users] Do Not See Extensions
 
I had a similar problem before.
Two potential workarounds that worked sporadically. So you can give it a try.
1) When the Extension manager popsup and keeps loading, right click to select "Go Back", and right again click to select "Go Foward". Repeat until the extensions show up (or give up when you are convinced this doesn't work).
2) Uninstall and re-install slicer

Timothy

>>> Emily Louise Belleau <[hidden email]> 02/24/15 12:26 PM >>>


Hello Slicer Users,


I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.


I checked the application settings and the extension manager is enabled.


Can anyone tell me what might be the problem?


Thanks,


Emily



This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation.

_______________________________________________
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[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.




--
Carol Johnson

Email: [hidden email]

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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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Re: Do Not See Extensions

Jean-Christophe Fillion-Robin
Hi Carol, Emily and Timothy,

Which version of Slicer and Operating System (Windows7, Windws8, .. ?) are you all using ?

Thanks
Jc

On Tue, Feb 24, 2015 at 4:28 PM, Carol Johnson <[hidden email]> wrote:
I have been having the same issues.
However, I just tried logging in as an administrator and using Internet Explorer as my browser, I was able to access the appstore with this link http://slicer.kitware.com/midas3/slicerappstore

Hope this helps
Carol

On Tue, Feb 24, 2015 at 2:31 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Users,


I am still having a problem installing the DTIPrep extension. I have tried all of the steps that Timothy has suggested (thanks Tim).


Any thoughts?


Emily


From: Timothy Yeung <[hidden email]>
Sent: Tuesday, February 24, 2015 11:31 AM
To: [hidden email]; Emily Louise Belleau
Subject: Re: [slicer-users] Do Not See Extensions
 
I had a similar problem before.
Two potential workarounds that worked sporadically. So you can give it a try.
1) When the Extension manager popsup and keeps loading, right click to select "Go Back", and right again click to select "Go Foward". Repeat until the extensions show up (or give up when you are convinced this doesn't work).
2) Uninstall and re-install slicer

Timothy

>>> Emily Louise Belleau <[hidden email]> 02/24/15 12:26 PM >>>


Hello Slicer Users,


I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.


I checked the application settings and the extension manager is enabled.


Can anyone tell me what might be the problem?


Thanks,


Emily



This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation.

_______________________________________________
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.




--
Carol Johnson

Email: [hidden email]

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The information in this e-mail is intended only for the person to whom it is
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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.




--
+1 919 869 8849

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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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Re: Do Not See Extensions

Timothy Yeung
Slicer 4.4.0. and 4.2.1.
Windows 7 Professional (x64-based PC)

Thanks
Timothy


>>> Jean-Christophe Fillion-Robin <[hidden email]> 02/25/15 6:13 PM >>>
Hi Carol, Emily and Timothy,

Which version of Slicer and Operating System (Windows7, Windws8, .. ?) are you all using ?

Thanks
Jc

On Tue, Feb 24, 2015 at 4:28 PM, Carol Johnson <[hidden email]> wrote:
I have been having the same issues.
However, I just tried logging in as an administrator and using Internet Explorer as my browser, I was able to access the appstore with this link http://slicer.kitware.com/midas3/slicerappstore

Hope this helps
Carol

On Tue, Feb 24, 2015 at 2:31 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Users,


I am still having a problem installing the DTIPrep extension. I have tried all of the steps that Timothy has suggested (thanks Tim).


Any thoughts?


Emily


From: Timothy Yeung <[hidden email]>
Sent: Tuesday, February 24, 2015 11:31 AM
To: [hidden email]; Emily Louise Belleau
Subject: Re: [slicer-users] Do Not See Extensions
 
I had a similar problem before.
Two potential workarounds that worked sporadically. So you can give it a try.
1) When the Extension manager popsup and keeps loading, right click to select "Go Back", and right again click to select "Go Foward". Repeat until the extensions show up (or give up when you are convinced this doesn't work).
2) Uninstall and re-install slicer

Timothy

>>> Emily Louise Belleau <[hidden email]> 02/24/15 12:26 PM >>>


Hello Slicer Users,


I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.


I checked the application settings and the extension manager is enabled.


Can anyone tell me what might be the problem?


Thanks,


Emily



This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation.

_______________________________________________
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.




--
Carol Johnson

Email: [hidden email]

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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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.




--
+1 919 869 8849


This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation.
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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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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Re: Do Not See Extensions

Carol Johnson
In reply to this post by Jean-Christophe Fillion-Robin
I am using Slicer 4.4 and 4.3.1
Windows 7 Professional  x64

As I mentioned, I cannot even access the website  ( http://slicer.kitware.com/midas3/slicerappstore ) unless I log in as an administrator and use Internet Explorer (v11). (It won't load with Firefox).

Carol

On Wed, Feb 25, 2015 at 6:12 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:
Hi Carol, Emily and Timothy,

Which version of Slicer and Operating System (Windows7, Windws8, .. ?) are you all using ?

Thanks
Jc

On Tue, Feb 24, 2015 at 4:28 PM, Carol Johnson <[hidden email]> wrote:
I have been having the same issues.
However, I just tried logging in as an administrator and using Internet Explorer as my browser, I was able to access the appstore with this link http://slicer.kitware.com/midas3/slicerappstore

Hope this helps
Carol

On Tue, Feb 24, 2015 at 2:31 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Users,


I am still having a problem installing the DTIPrep extension. I have tried all of the steps that Timothy has suggested (thanks Tim).


Any thoughts?


Emily


From: Timothy Yeung <[hidden email]>
Sent: Tuesday, February 24, 2015 11:31 AM
To: [hidden email]; Emily Louise Belleau
Subject: Re: [slicer-users] Do Not See Extensions
 
I had a similar problem before.
Two potential workarounds that worked sporadically. So you can give it a try.
1) When the Extension manager popsup and keeps loading, right click to select "Go Back", and right again click to select "Go Foward". Repeat until the extensions show up (or give up when you are convinced this doesn't work).
2) Uninstall and re-install slicer

Timothy

>>> Emily Louise Belleau <[hidden email]> 02/24/15 12:26 PM >>>


Hello Slicer Users,


I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.


I checked the application settings and the extension manager is enabled.


Can anyone tell me what might be the problem?


Thanks,


Emily



This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation.

_______________________________________________
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.




--
Carol Johnson

Email: [hidden email]

_______________________________________________
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[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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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.




--
<a href="tel:%2B1%20919%20869%208849" value="+19198698849" target="_blank">+1 919 869 8849



--
Carol Johnson

Email: [hidden email]

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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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.
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Re: Do Not See Extensions

Andras Lasso-2

The problem is most probably caused by the extreme firewall/proxy settings enforced on your computer.

 

If the slicerappstore webpage fails to load on firefox or chrome then it won’t be accessible to any other software, such as 3D Slicer either. You either have to contact your IT administrators to allow web access to applications on your computer or download all the extensions that you need in the allowed web broswer and install it manually as described here:

 

http://www.slicer.org/slicerWiki/index.php/Documentation/4.4/FAQ#How_to_manually_download_an_extension_package.3F

and

http://www.slicer.org/slicerWiki/index.php/Documentation/4.4/FAQ#How_to_manually_install_an_extension.3F

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Carol Johnson
Sent: Thursday, February 26, 2015 10:20 AM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]; Timothy Yeung
Subject: Re: [slicer-users] Do Not See Extensions

 

I am using Slicer 4.4 and 4.3.1

Windows 7 Professional  x64

 

As I mentioned, I cannot even access the website  ( http://slicer.kitware.com/midas3/slicerappstore ) unless I log in as an administrator and use Internet Explorer (v11). (It won't load with Firefox).

Carol

 

On Wed, Feb 25, 2015 at 6:12 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Carol, Emily and Timothy,

Which version of Slicer and Operating System (Windows7, Windws8, .. ?) are you all using ?

Thanks

Jc

 

On Tue, Feb 24, 2015 at 4:28 PM, Carol Johnson <[hidden email]> wrote:

I have been having the same issues.

However, I just tried logging in as an administrator and using Internet Explorer as my browser, I was able to access the appstore with this link http://slicer.kitware.com/midas3/slicerappstore

Then you can do a manual download and  install of the package. See
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ#How_to_manually_install_an_extension_.3F

 

Hope this helps

Carol

 

On Tue, Feb 24, 2015 at 2:31 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Users,

 

I am still having a problem installing the DTIPrep extension. I have tried all of the steps that Timothy has suggested (thanks Tim).

 

Any thoughts?

 

Emily


From: Timothy Yeung <[hidden email]>
Sent: Tuesday, February 24, 2015 11:31 AM
To: [hidden email]; Emily Louise Belleau
Subject: Re: [slicer-users] Do Not See Extensions

 

I had a similar problem before.
Two potential workarounds that worked sporadically. So you can give it a try.
1) When the Extension manager popsup and keeps loading, right click to select "Go Back", and right again click to select "Go Foward". Repeat until the extensions show up (or give up when you are convinced this doesn't work).
2) Uninstall and re-install slicer

Timothy

>>> Emily Louise Belleau <[hidden email]> 02/24/15 12:26 PM >>>

 

Hello Slicer Users,

 

I had previously had downloaded DTIPrep and DTIProcess through the extensions manager is Slicer. Now, I no longer see them. In fact, no extensions are available to download.

 

I checked the application settings and the extension manager is enabled.

 

Can anyone tell me what might be the problem?

 

Thanks,

 

Emily

 


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