Segmentation violation on BasicNavigation tutorial

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Segmentation violation on BasicNavigation tutorial

Rafael Palomar
Hello,

I'm trying to follow the BasicNavigation tutorial of the Slicer wiki (http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).

There is a moment in wich I have to set the driver for the red slice to locator, in the OpenIGTLink module. An then I get a segmentation violation error and Slicer3 crashes. I am using Slicer 3.4.2.

Does anyone completed successfully this tutorial? Any Idea?

Thanks in advance.

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Re: Segmentation violation on BasicNavigation tutorial

Anka Kochanowska
Hi!
I had the same problem. This happens because the tutorial tells you to remove calibration matrix and at that time Tracker is under calibration and is removed altogether. Before deleting calibration, drag out the Tracker or next time do not do calibration at all.
Anka


On Fri, Jun 4, 2010 at 7:11 AM, Rafael Palomar <[hidden email]> wrote:
Hello,

I'm trying to follow the BasicNavigation tutorial of the Slicer wiki (http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).

There is a moment in wich I have to set the driver for the red slice to locator, in the OpenIGTLink module. An then I get a segmentation violation error and Slicer3 crashes. I am using Slicer 3.4.2.

Does anyone completed successfully this tutorial? Any Idea?

Thanks in advance.

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


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Re: Segmentation violation on BasicNavigation tutorial

swallace
In reply to this post by Rafael Palomar
Hi Rafael,

I had no problems with using it in 3.5, but am happy to try to reproduce
you problem in 3.4.

Which OS are you using, and could you also pass along any error messages
that popped up?

Thanks,

Stuart

> Hello,
>
> I'm trying to follow the BasicNavigation tutorial of the Slicer wiki (
> http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).
>
> There is a moment in wich I have to set the driver for the red slice to
> locator, in the OpenIGTLink module. An then I get a segmentation violation
> error and Slicer3 crashes. I am using Slicer 3.4.2.
>
> Does anyone completed successfully this tutorial? Any Idea?
>
> Thanks in advance.
> _______________________________________________
> 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

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Fwd: Segmentation violation on BasicNavigation tutorial

Rafael Palomar


---------- Forwarded message ----------
From: Rafael Palomar <[hidden email]>
Date: 2010/6/4
Subject: Re: [slicer-users] Segmentation violation on BasicNavigation tutorial
To: [hidden email]


Hi,

ok, I will give you more accurate information.

The version I am using is 3.4.3-2010-03-23 for linux 32-bits.

You could reach the same error in this way:

1. Load abdominal atlas.
2. Open OpenIGTLink module.
3. Add a connector, set it as server and make it active
4. Run the tracker client
5. Change red driver in visualization/slicer control->Driver to Locator instead User

Finally I get this output:

child killed: segmentation violation
 
CHILDKILLED 6001 SIGSEGV {segmentation violation

Thank you. Best regards,
Rafael Palomar.

2010/6/4 <[hidden email]>

Hi Rafael,

I had no problems with using it in 3.5, but am happy to try to reproduce
you problem in 3.4.

Which OS are you using, and could you also pass along any error messages
that popped up?

Thanks,

Stuart

> Hello,
>
> I'm trying to follow the BasicNavigation tutorial of the Slicer wiki (
> http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).
>
> There is a moment in wich I have to set the driver for the red slice to
> locator, in the OpenIGTLink module. An then I get a segmentation violation
> error and Slicer3 crashes. I am using Slicer 3.4.2.
>
> Does anyone completed successfully this tutorial? Any Idea?
>
> Thanks in advance.
> _______________________________________________
> 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



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: Fwd: Segmentation violation on BasicNavigation tutorial

Anka Kochanowska
Hi!
Have you checked in the module data if the Tracker was added?
Have you seen the transformation changed?
In OpenIGTLinkIF you have to set Tracker(POSITION) as locator source.

Today I was not able to connect on Slicer default port 18944, so I defined a different port - 10001.
You have to define port before activating server and make sure you press return  after entering port number, otherwise it goes back to default :-)


I have Slicer 3.41.0 and 3.6 RC2 1.0

Anka


On Mon, Jun 7, 2010 at 4:26 AM, Rafael Palomar <[hidden email]> wrote:


---------- Forwarded message ----------
From: Rafael Palomar <[hidden email]>
Date: 2010/6/4
Subject: Re: [slicer-users] Segmentation violation on BasicNavigation tutorial
To: [hidden email]


Hi,

ok, I will give you more accurate information.

The version I am using is 3.4.3-2010-03-23 for linux 32-bits.

You could reach the same error in this way:

1. Load abdominal atlas.
2. Open OpenIGTLink module.
3. Add a connector, set it as server and make it active
4. Run the tracker client
5. Change red driver in visualization/slicer control->Driver to Locator instead User

Finally I get this output:

child killed: segmentation violation
 
CHILDKILLED 6001 SIGSEGV {segmentation violation

Thank you. Best regards,
Rafael Palomar.

2010/6/4 <[hidden email]>

Hi Rafael,

I had no problems with using it in 3.5, but am happy to try to reproduce
you problem in 3.4.

Which OS are you using, and could you also pass along any error messages
that popped up?

Thanks,

Stuart

> Hello,
>
> I'm trying to follow the BasicNavigation tutorial of the Slicer wiki (
> http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).
>
> There is a moment in wich I have to set the driver for the red slice to
> locator, in the OpenIGTLink module. An then I get a segmentation violation
> error and Slicer3 crashes. I am using Slicer 3.4.2.
>
> Does anyone completed successfully this tutorial? Any Idea?
>
> Thanks in advance.
> _______________________________________________
> 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



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: Fwd: Segmentation violation on BasicNavigation tutorial

Haiying Liu
Hi Rafael,

Would you mind sending me the debugging messages? On Linux, try to do
the following:

1. cd to Slicer3-build/bin
2. gdb ./Slicer3-real
3. run
4. use Slicer3 as you described before
5. When Slicer crashed, go to the same command window and run "bt"
6. hit "return" until you have no more messages
7. save all debug messages and send a copy to me

I will look at what caused the crash.

Thank you very much,


Haiying

>
>
>
> On Mon, Jun 7, 2010 at 4:26 AM, Rafael Palomar
> <[hidden email] <mailto:[hidden email]>>
> wrote:
>
>
>
>     ---------- Forwarded message ----------
>     From: *Rafael Palomar* <[hidden email]
>     <mailto:[hidden email]>>
>     Date: 2010/6/4
>     Subject: Re: [slicer-users] Segmentation violation on
>     BasicNavigation tutorial
>     To: [hidden email] <mailto:[hidden email]>
>
>
>     Hi,
>
>     ok, I will give you more accurate information.
>
>     The version I am using is 3.4.3-2010-03-23 for linux 32-bits.
>
>     You could reach the same error in this way:
>
>     1. Load abdominal atlas.
>     2. Open OpenIGTLink module.
>     3. Add a connector, set it as server and make it active
>     4. Run the tracker client
>     5. Change red driver in visualization/slicer control->Driver to
>     Locator instead User
>
>     Finally I get this output:
>
>     child killed: segmentation violation
>      
>     CHILDKILLED 6001 SIGSEGV {segmentation violation
>
>     Thank you. Best regards,
>     Rafael Palomar.
>
>     2010/6/4 <[hidden email]
>     <mailto:[hidden email]>>
>
>         Hi Rafael,
>
>         I had no problems with using it in 3.5, but am happy to try to
>         reproduce
>         you problem in 3.4.
>
>         Which OS are you using, and could you also pass along any
>         error messages
>         that popped up?
>
>         Thanks,
>
>         Stuart
>
>         > Hello,
>         >
>         > I'm trying to follow the BasicNavigation tutorial of the
>         Slicer wiki (
>         > http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).
>         >
>         > There is a moment in wich I have to set the driver for the
>         red slice to
>         > locator, in the OpenIGTLink module. An then I get a
>         segmentation violation
>         > error and Slicer3 crashes. I am using Slicer 3.4.2.
>         >
>         > Does anyone completed successfully this tutorial? Any Idea?
>         >
>         > Thanks in advance.
>         > _______________________________________________
>         > slicer-users mailing list
>         > [hidden email]
>         <mailto:[hidden email]>
>         > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>         > To unsubscribe: send email to
>         > [hidden email]
>         <mailto:[hidden email]> with
>         unsubscribe as the
>         > subject
>
>
>
>         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] <mailto:[hidden email]>
>     http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>     To unsubscribe: send email to
>     [hidden email]
>     <mailto:[hidden email]> with
>     unsubscribe as the subject
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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

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Re: Fwd: Segmentation violation on BasicNavigation tutorial

swallace
In reply to this post by Rafael Palomar
Hi Rafael,

Just wanted to say I havent forgotten your issues, and will try to
reproduce them after I meet some 3.6 release related deadlines.

Thanks for your patience, and thanks to everyone chipping in their
suggestions!

Stuart

> ---------- Forwarded message ----------
> From: Rafael Palomar <[hidden email]>
> Date: 2010/6/4
> Subject: Re: [slicer-users] Segmentation violation on BasicNavigation
> tutorial
> To: [hidden email]
>
>
> Hi,
>
> ok, I will give you more accurate information.
>
> The version I am using is 3.4.3-2010-03-23 for linux 32-bits.
>
> You could reach the same error in this way:
>
> 1. Load abdominal atlas.
> 2. Open OpenIGTLink module.
> 3. Add a connector, set it as server and make it active
> 4. Run the tracker client
> 5. Change red driver in visualization/slicer control->Driver to Locator
> instead User
>
> Finally I get this output:
>
> child killed: segmentation violation
>
> CHILDKILLED 6001 SIGSEGV {segmentation violation
>
> Thank you. Best regards,
> Rafael Palomar.
>
> 2010/6/4 <[hidden email]>
>
> Hi Rafael,
>>
>> I had no problems with using it in 3.5, but am happy to try to reproduce
>> you problem in 3.4.
>>
>> Which OS are you using, and could you also pass along any error messages
>> that popped up?
>>
>> Thanks,
>>
>> Stuart
>>
>> > Hello,
>> >
>> > I'm trying to follow the BasicNavigation tutorial of the Slicer wiki (
>> > http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).
>> >
>> > There is a moment in wich I have to set the driver for the red slice
>> to
>> > locator, in the OpenIGTLink module. An then I get a segmentation
>> violation
>> > error and Slicer3 crashes. I am using Slicer 3.4.2.
>> >
>> > Does anyone completed successfully this tutorial? Any Idea?
>> >
>> > Thanks in advance.
>> > _______________________________________________
>> > 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
>>
>>
>>
>> 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

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Re: Fwd: Segmentation violation on BasicNavigation tutorial

Rafael Palomar
In reply to this post by Anka Kochanowska
Hi!

I did set up the locator source in OpenIGTLinkIF to Tracker(POSITION) and works fine!!

Thank all for your help!


2010/6/7 Anka Kochanowska <[hidden email]>
Hi!
Have you checked in the module data if the Tracker was added?
Have you seen the transformation changed?
---->In OpenIGTLinkIF you have to set Tracker(POSITION) as locator source.<----

Today I was not able to connect on Slicer default port 18944, so I defined a different port - 10001.
You have to define port before activating server and make sure you press return  after entering port number, otherwise it goes back to default :-)


I have Slicer 3.41.0 and 3.6 RC2 1.0

Anka



On Mon, Jun 7, 2010 at 4:26 AM, Rafael Palomar <[hidden email]> wrote:


---------- Forwarded message ----------
From: Rafael Palomar <[hidden email]>
Date: 2010/6/4
Subject: Re: [slicer-users] Segmentation violation on BasicNavigation tutorial
To: [hidden email]


Hi,

ok, I will give you more accurate information.

The version I am using is 3.4.3-2010-03-23 for linux 32-bits.

You could reach the same error in this way:

1. Load abdominal atlas.
2. Open OpenIGTLink module.
3. Add a connector, set it as server and make it active
4. Run the tracker client
5. Change red driver in visualization/slicer control->Driver to Locator instead User

Finally I get this output:

child killed: segmentation violation
 
CHILDKILLED 6001 SIGSEGV {segmentation violation

Thank you. Best regards,
Rafael Palomar.

2010/6/4 <[hidden email]>

Hi Rafael,

I had no problems with using it in 3.5, but am happy to try to reproduce
you problem in 3.4.

Which OS are you using, and could you also pass along any error messages
that popped up?

Thanks,

Stuart

> Hello,
>
> I'm trying to follow the BasicNavigation tutorial of the Slicer wiki (
> http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training).
>
> There is a moment in wich I have to set the driver for the red slice to
> locator, in the OpenIGTLink module. An then I get a segmentation violation
> error and Slicer3 crashes. I am using Slicer 3.4.2.
>
> Does anyone completed successfully this tutorial? Any Idea?
>
> Thanks in advance.
> _______________________________________________
> 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



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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