Slicer Brain Automatic Segmentation

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Slicer Brain Automatic Segmentation

Michelle Farley
Hi everyone,
I’m new to slicer for human MR imaging.  I’d like to use the automatic segmentation feature for the human brain with skull.  I’m following the tutorials but I’m getting a "processing did not execute correctly error" pop up then a "segmentation did not execute correctly" error pop up.  I’m running slicer 4.3.1 on OS X, 10.9.2.  Any insight would be much appreciated.

Thanks in advance,
Michelle  


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Viz
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Re: Slicer Brain Automatic Segmentation

Viz
This post was updated on .
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Re: Slicer Brain Automatic Segmentation

Michelle Farley
Thanks so much for replying.  I think I wasn¹t clear on my question.  I¹m
looking to use the slicer brain atlas to map my T1w (or T2w) scan to the
brain anatomical structures.  This is the functionality that isn¹t working
for me and Will.  

Thanks again,
Michelle  




On 5/8/14, 3:03 PM, "vizproguy" <[hidden email]> wrote:

>Hi Michelle,
>
>Please refer to
>
>For manual segmentation, please see 48:30 into the video :
>http://vimeo.com/37671358 <http://vimeo.com/37671358>
>
>For automatic segmentation :
>https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/
>CarreraSliceInteractiveSegmenter
><https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules
>/CarreraSliceInteractiveSegmenter>
>
>&
>
>http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/K
>SliceInteractiveSegmenter
><http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/
>KSliceInteractiveSegmenter>
>
>
>
>--
>View this message in context:
>http://slicer-users.65878.n3.nabble.com/Slicer-Brain-Automatic-Segmentatio
>n-tp4027630p4027631.html
>Sent from the slicer-users mailing list archive at Nabble.com.
>_______________________________________________
>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.
>


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Re: Slicer Brain Automatic Segmentation

Michelle Farley
I’m going to ask my question a little differently.  Is there anyone
currently using the brain automatic segmentation atlas?  If you could I
take 5 minutes of your time for you to show me how you use it.  There is a
good chance my problem is due to my lack on understanding and not a bug in
slicer.  

All help is appreciated!
Michelle




On 5/8/14, 3:19 PM, "Michelle Farley" <[hidden email]> wrote:

>Thanks so much for replying.  I think I wasn¹t clear on my question.  I¹m
>looking to use the slicer brain atlas to map my T1w (or T2w) scan to the
>brain anatomical structures.  This is the functionality that isn¹t working
>for me and Will.  
>
>Thanks again,
>Michelle  
>
>
>
>
>On 5/8/14, 3:03 PM, "vizproguy" <[hidden email]> wrote:
>
>>Hi Michelle,
>>
>>Please refer to
>>
>>For manual segmentation, please see 48:30 into the video :
>>http://vimeo.com/37671358 <http://vimeo.com/37671358>
>>
>>For automatic segmentation :
>>https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules
>>/
>>CarreraSliceInteractiveSegmenter
>><https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Module
>>s
>>/CarreraSliceInteractiveSegmenter>
>>
>>&
>>
>>http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/
>>K
>>SliceInteractiveSegmenter
>><http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules
>>/
>>KSliceInteractiveSegmenter>
>>
>>
>>
>>--
>>View this message in context:
>>http://slicer-users.65878.n3.nabble.com/Slicer-Brain-Automatic-Segmentati
>>o
>>n-tp4027630p4027631.html
>>Sent from the slicer-users mailing list archive at Nabble.com.
>>_______________________________________________
>>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.
>>
>
>
>_______________________________________________
>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


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Re: Slicer Brain Automatic Segmentation

Kilian Pohl
In reply to this post by Michelle Farley
Hi everyone,
I’m new to slicer for human MR imaging.  I’d like to use the automatic segmentation feature for the human brain with skull.  I’m following the tutorials but I’m getting a "processing did not execute correctly error" pop up then a "segmentation did not execute correctly" error pop up.  I’m running slicer 4.3.1 on OS X, 10.9.2.  Any insight would be much appreciated.

Thanks in advance,
Michelle  



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-- 
Kilian M. Pohl, Ph.D. 

Senior Research Scientist
SRI International

Consulting Assistant Professor
Department of Psychiatry & Behavioral Sciences
Stanford University

333 Ravenswood Ave
Menlo Park, CA 94025 

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Re: Slicer Brain Automatic Segmentation

Michelle Farley
Hi Killian,
Here is the attached bug report.  Please let me know if there is any thing else I can help you with.  

Thanks so much!
Michelle

From: Kilian Pohl <[hidden email]>
Date: Friday, May 9, 2014 at 12:32 PM
To: <[hidden email]>
Subject: Re: [slicer-users] Slicer Brain Automatic Segmentation

Hi everyone,
I’m new to slicer for human MR imaging.  I’d like to use the automatic segmentation feature for the human brain with skull.  I’m following the tutorials but I’m getting a "processing did not execute correctly error" pop up then a "segmentation did not execute correctly" error pop up.  I’m running slicer 4.3.1 on OS X, 10.9.2.  Any insight would be much appreciated.

Thanks in advance,
Michelle  



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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
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.


--
Kilian M. Pohl, Ph.D.

Senior Research Scientist
SRI International

Consulting Assistant Professor
Department of Psychiatry & Behavioral Sciences
Stanford University

333 Ravenswood Ave
Menlo Park, CA 94025
_______________________________________________ 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.

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slicer_EMSegmenterwithAtlas Bug Report.rtf (42K) Download Attachment