Fwd: Re: VMTK Slicer4 problem?

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Fwd: Re: VMTK Slicer4 problem?

Kikinis, Ron,M.D.
Hi,

I have added the slicer user mailing list, since this is of potential
general interest. We had a version of vmtk integrated with slicer in an
earlier version of Slicer. We are in the process of porting to the
current version of Slicer.

1. Search for vmtk in the following page:
http://www.slicer.org/slicerWiki/index.php/Documentation-3.6
2. To download 3.6: http://www.slicer.org/pages/Special:SlicerDownloads

Ron




-------- Original Message --------
Subject: Re: VMTK Slicer4 problem?
Date: Wed, 16 Apr 2014 08:38:19 -0400
From: Steve Pieper <[hidden email]>


Hi Ron -

I believe we are "close" to a solution - the VMTK extension works great
on local builds, and Jc knows how to fix the extension loading issues
that have stumped the rest of us for a couple years now.  @Jc can you
give an update on that?

-Steve


On Wed, Apr 16, 2014 at 8:19 AM, Ron Kikinis <[hidden email]
<mailto:[hidden email]>> wrote:



     Sent from my mobile phone.

     Begin forwarded message:

>     *Date:* April 16, 2014 at 1:30:27 AM MDT
...
>     *To:* "[hidden email] <mailto:[hidden email]>"
>     <[hidden email] <mailto:[hidden email]>>
>     *Subject:* *VMTK Slicer4 problem?*
>
>     Dear Dr Ron Kikinis
>
....

>     I am busy conducting my research on hemispheric lateralisation and
>     its relationship with asymmetry of the carotid arteries. The
>     supervisor for my thesis is Professor Mark Solms (head of the
>     Psychology Department).
>     I really want to use Slicer4 3D with the vascular modeling toolkit
>     for the geometric analysis of my thesis, but I am really
>     struggling to make it work. My DICOM database consists of CTAngios
>     of the head and neck ( and I have Windows 64-bit laptop).
>     I have downloaded the slicer program, and have downloaded the VMTK
>     from thier website, but I have no idea how to make the two work
>     with one another. I am struggling to understand the instructions
>     in the Wiki forum (since I have no experience with computer
>     programs like this). I have approached the computer science
>     department and they are also unsure.
>
>     I apologise for the inconvenience and realise you are very busy.
>     I would appreciate any help you can give me.
>
>     Sincerely
>     Anica
>
>     Sent from my iPad

     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.



--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


_______________________________________________
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: Fwd: Re: VMTK Slicer4 problem?

arumiat
Depending on how urgent it is for the user I've a native VMTK 'cribsheet' I'm happy to share w exact commands/pypes to run for vascular level set segmentation from a CT angio series. I've also no computing background/ command-line experience but still manage to use it with some success. Of course once the Slicer extension is working this would be the ideal
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Re: Fwd: Re: VMTK Slicer4 problem?

Anica
That would be amazing! I am hoping to start the analysis before the end of
the month.

Thank you for your reply.
I have installed the new one (the older version that was recommended), but
now, the extension button doesn't work.
When I click onto the extension icon and then "next" it says "Cannot connect
to the specified repository, check network connection".
I have been trying to solve this for about 5 hours. I don't know what to do.
(I reinstalled python, vmtk etc to try see if that helped)
My connection is fine. I took my windows firewall off and it changed
nothing.
Am I missing something? Maybe its something simple that I just don't know
about?
I am so frustrated. I don't understand allot of computer jargon so its a bit
difficult to follow most of the forums.
I also tried to download the vmtk zip file from that GIB place and copied
all the folders into the "modules" folder in slicer 3. But that hasn't
worked. Not sure if I was supposed to only copy some of them and not all of
them? or was meant to make a special folder?
Any help would be greatly appreciated!
Thanks
Anica
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Re: Fwd: Re: VMTK Slicer4 problem?

arumiat
Arnica

I tried as you did with getting it to work with 3.6 but I don't think the extension server is running properly anymore.

Apparently it will work w Slicer 4 if you compile from source code (whatever that means) so I take it that's out for you too!

I just had an email from JC who is working on the vmtk extension and he thinks the extension in slicer 4 may be up for next week

If you don't want to wait that long (&often no doubt code throws up problems that might make it longer) you can download the vmtk standalone from Vmtk.org and learn to use that. Looks v.intimidating but once you get the hang of is okay. I'll send you my crib sheet for basically what you type into the console tmw or you can search out my threads on VMTK users.  I even plan to use it tomorrow & we can sort of some remote viewing if you're free &that's helpful
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Re: VMTK Slicer4 problem?

Anica
Dear Arumiat
Thank you so much for your reply.
That is great news about slicer 4! If the extension for slicer 4 will work around next week I will try it then.
But I will try see if I can use it alone so long (just incase).
I look forward to the cribsheet- thank you so much for offering that. I am not 100% sure what remote viewing is(i think its when you link to my computer?), and dont know how to do it, but if I cant get some progress with the sheet I will contact you again- is that ok?

Sincerely
Anica

Sent from my iPad

On 17 Apr 2014, at 10:11 PM, "arumiat [via slicer-users]" <[hidden email]> wrote:

Arnica

I tried as you did with getting it to work with 3.6 but I don't think the extension server is running properly anymore.

Apparently it will work w Slicer 4 if you compile from source code (whatever that means) so I take it that's out for you too!

I just had an email from JC who is working on the vmtk extension and he thinks the extension in slicer 4 may be up for next week

If you don't want to wait that long (&often no doubt code throws up problems that might make it longer) you can download the vmtk standalone from Vmtk.org and learn to use that. Looks v.intimidating but once you get the hang of is okay. I'll send you my crib sheet for basically what you type into the console tmw or you can search out my threads on VMTK users.  I even plan to use it tomorrow & we can sort of some remote viewing if you're free &that's helpful


If you reply to this email, your message will be added to the discussion below:
http://slicer-users.65878.n3.nabble.com/Fwd-Re-VMTK-Slicer4-problem-tp4027514p4027532.html
To unsubscribe from Fwd: Re: VMTK Slicer4 problem?, click here.
NAML
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Re: VMTK Slicer4 problem?

Jean-Christophe Fillion-Robin
Hi Folks,

As I replied here [1], I just updated the VMTK extension. After downloading tomorrow nightly and installing the extension, let me know if you experience any issue.

Thanks
Jc

[1] http://slicer-users.65878.n3.nabble.com/Vmtk-extension-tp4027652p4027668.html


On Fri, Apr 18, 2014 at 3:25 AM, Anica <[hidden email]> wrote:
Dear Arumiat
Thank you so much for your reply.
That is great news about slicer 4! If the extension for slicer 4 will work around next week I will try it then.
But I will try see if I can use it alone so long (just incase).
I look forward to the cribsheet- thank you so much for offering that. I am not 100% sure what remote viewing is(i think its when you link to my computer?), and dont know how to do it, but if I cant get some progress with the sheet I will contact you again- is that ok?

Sincerely
Anica

Sent from my iPad

On 17 Apr 2014, at 10:11 PM, "arumiat [via slicer-users]" <[hidden email]> wrote:

Arnica

I tried as you did with getting it to work with 3.6 but I don't think the extension server is running properly anymore.

Apparently it will work w Slicer 4 if you compile from source code (whatever that means) so I take it that's out for you too!

I just had an email from JC who is working on the vmtk extension and he thinks the extension in slicer 4 may be up for next week

If you don't want to wait that long (&often no doubt code throws up problems that might make it longer) you can download the vmtk standalone from Vmtk.org and learn to use that. Looks v.intimidating but once you get the hang of is okay. I'll send you my crib sheet for basically what you type into the console tmw or you can search out my threads on VMTK users.  I even plan to use it tomorrow & we can sort of some remote viewing if you're free &that's helpful


If you reply to this email, your message will be added to the discussion below:
http://slicer-users.65878.n3.nabble.com/Fwd-Re-VMTK-Slicer4-problem-tp4027514p4027532.html
To unsubscribe from Fwd: Re: VMTK Slicer4 problem?, click here.
NAML


View this message in context: Re: VMTK Slicer4 problem?

Sent from the slicer-users mailing list archive at Nabble.com.

_______________________________________________
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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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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
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Fwd: Re: VMTK Slicer4 problem?

madanrao
In reply to this post by Kikinis, Ron,M.D.
Hi,

Daniel Haehn has developed VMTK module for Slicer as an application for coronary arteries.Therefore, VMTK was standardized for coronaries and lot of online information is available (some links below). I assume you need to work on coronaries first and get a first hand experience before you venture with cerebral arteries.



AM Mohan Rao


On Wed, Apr 16, 2014 at 6:17 PM, Ron Kikinis <[hidden email]> wrote:
Hi,

I have added the slicer user mailing list, since this is of potential
general interest. We had a version of vmtk integrated with slicer in an
earlier version of Slicer. We are in the process of porting to the
current version of Slicer.

1. Search for vmtk in the following page:
http://www.slicer.org/slicerWiki/index.php/Documentation-3.6
2. To download 3.6: http://www.slicer.org/pages/Special:SlicerDownloads

Ron




-------- Original Message --------
Subject:        Re: VMTK Slicer4 problem?
Date:   Wed, 16 Apr 2014 08:38:19 -0400
From:   Steve Pieper <[hidden email]>


Hi Ron -

I believe we are "close" to a solution - the VMTK extension works great
on local builds, and Jc knows how to fix the extension loading issues
that have stumped the rest of us for a couple years now.  @Jc can you
give an update on that?

-Steve


On Wed, Apr 16, 2014 at 8:19 AM, Ron Kikinis <[hidden email]
<mailto:[hidden email]>> wrote:



     Sent from my mobile phone.

     Begin forwarded message:

>     *Date:* April 16, 2014 at 1:30:27 AM MDT
...
>     *To:* "[hidden email] <mailto:[hidden email]>"
>     <[hidden email] <mailto:[hidden email]>>
>     *Subject:* *VMTK Slicer4 problem?*
>
>     Dear Dr Ron Kikinis
>
....

>     I am busy conducting my research on hemispheric lateralisation and
>     its relationship with asymmetry of the carotid arteries. The
>     supervisor for my thesis is Professor Mark Solms (head of the
>     Psychology Department).
>     I really want to use Slicer4 3D with the vascular modeling toolkit
>     for the geometric analysis of my thesis, but I am really
>     struggling to make it work. My DICOM database consists of CTAngios
>     of the head and neck ( and I have Windows 64-bit laptop).
>     I have downloaded the slicer program, and have downloaded the VMTK
>     from thier website, but I have no idea how to make the two work
>     with one another. I am struggling to understand the instructions
>     in the Wiki forum (since I have no experience with computer
>     programs like this). I have approached the computer science
>     department and they are also unsure.
>
>     I apologise for the inconvenience and realise you are very busy.
>     I would appreciate any help you can give me.
>
>     Sincerely
>     Anica
>
>     Sent from my iPad

     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.



--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


_______________________________________________
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.
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Re: Fwd: Re: VMTK Slicer4 problem?

Steve Pieper-2
Looks like there was a build error on the vmtk extension last night, so it'll take another round of debugging before it's in the nightly.  Sorry for the delay.

-Steve


On Wed, May 14, 2014 at 2:30 AM, Madan Rao <[hidden email]> wrote:
Hi,

Daniel Haehn has developed VMTK module for Slicer as an application for coronary arteries.Therefore, VMTK was standardized for coronaries and lot of online information is available (some links below). I assume you need to work on coronaries first and get a first hand experience before you venture with cerebral arteries.



AM Mohan Rao


On Wed, Apr 16, 2014 at 6:17 PM, Ron Kikinis <[hidden email]> wrote:
Hi,

I have added the slicer user mailing list, since this is of potential
general interest. We had a version of vmtk integrated with slicer in an
earlier version of Slicer. We are in the process of porting to the
current version of Slicer.

1. Search for vmtk in the following page:
http://www.slicer.org/slicerWiki/index.php/Documentation-3.6
2. To download 3.6: http://www.slicer.org/pages/Special:SlicerDownloads

Ron




-------- Original Message --------
Subject:        Re: VMTK Slicer4 problem?
Date:   Wed, 16 Apr 2014 08:38:19 -0400
From:   Steve Pieper <[hidden email]>


Hi Ron -

I believe we are "close" to a solution - the VMTK extension works great
on local builds, and Jc knows how to fix the extension loading issues
that have stumped the rest of us for a couple years now.  @Jc can you
give an update on that?

-Steve


On Wed, Apr 16, 2014 at 8:19 AM, Ron Kikinis <[hidden email]
<mailto:[hidden email]>> wrote:



     Sent from my mobile phone.

     Begin forwarded message:

>     *Date:* April 16, 2014 at 1:30:27 AM MDT
...
>     *To:* "[hidden email] <mailto:[hidden email]>"
>     <[hidden email] <mailto:[hidden email]>>
>     *Subject:* *VMTK Slicer4 problem?*
>
>     Dear Dr Ron Kikinis
>
....

>     I am busy conducting my research on hemispheric lateralisation and
>     its relationship with asymmetry of the carotid arteries. The
>     supervisor for my thesis is Professor Mark Solms (head of the
>     Psychology Department).
>     I really want to use Slicer4 3D with the vascular modeling toolkit
>     for the geometric analysis of my thesis, but I am really
>     struggling to make it work. My DICOM database consists of CTAngios
>     of the head and neck ( and I have Windows 64-bit laptop).
>     I have downloaded the slicer program, and have downloaded the VMTK
>     from thier website, but I have no idea how to make the two work
>     with one another. I am struggling to understand the instructions
>     in the Wiki forum (since I have no experience with computer
>     programs like this). I have approached the computer science
>     department and they are also unsure.
>
>     I apologise for the inconvenience and realise you are very busy.
>     I would appreciate any help you can give me.
>
>     Sincerely
>     Anica
>
>     Sent from my iPad

     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.



--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


_______________________________________________
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.



_______________________________________________
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: Fwd: Re: VMTK Slicer4 problem?

Jean-Christophe Fillion-Robin


On Wed, May 14, 2014 at 7:24 AM, Steve Pieper <[hidden email]> wrote:
Looks like there was a build error on the vmtk extension last night, so it'll take another round of debugging before it's in the nightly.  Sorry for the delay.

-Steve


On Wed, May 14, 2014 at 2:30 AM, Madan Rao <[hidden email]> wrote:
Hi,

Daniel Haehn has developed VMTK module for Slicer as an application for coronary arteries.Therefore, VMTK was standardized for coronaries and lot of online information is available (some links below). I assume you need to work on coronaries first and get a first hand experience before you venture with cerebral arteries.



AM Mohan Rao


On Wed, Apr 16, 2014 at 6:17 PM, Ron Kikinis <[hidden email]> wrote:
Hi,

I have added the slicer user mailing list, since this is of potential
general interest. We had a version of vmtk integrated with slicer in an
earlier version of Slicer. We are in the process of porting to the
current version of Slicer.

1. Search for vmtk in the following page:
http://www.slicer.org/slicerWiki/index.php/Documentation-3.6
2. To download 3.6: http://www.slicer.org/pages/Special:SlicerDownloads

Ron




-------- Original Message --------
Subject:        Re: VMTK Slicer4 problem?
Date:   Wed, 16 Apr 2014 08:38:19 -0400
From:   Steve Pieper <[hidden email]>


Hi Ron -

I believe we are "close" to a solution - the VMTK extension works great
on local builds, and Jc knows how to fix the extension loading issues
that have stumped the rest of us for a couple years now.  @Jc can you
give an update on that?

-Steve


On Wed, Apr 16, 2014 at 8:19 AM, Ron Kikinis <[hidden email]
<mailto:[hidden email]>> wrote:



     Sent from my mobile phone.

     Begin forwarded message:

>     *Date:* April 16, 2014 at 1:30:27 AM MDT
...
>     *To:* "[hidden email] <mailto:[hidden email]>"
>     <[hidden email] <mailto:[hidden email]>>
>     *Subject:* *VMTK Slicer4 problem?*
>
>     Dear Dr Ron Kikinis
>
....

>     I am busy conducting my research on hemispheric lateralisation and
>     its relationship with asymmetry of the carotid arteries. The
>     supervisor for my thesis is Professor Mark Solms (head of the
>     Psychology Department).
>     I really want to use Slicer4 3D with the vascular modeling toolkit
>     for the geometric analysis of my thesis, but I am really
>     struggling to make it work. My DICOM database consists of CTAngios
>     of the head and neck ( and I have Windows 64-bit laptop).
>     I have downloaded the slicer program, and have downloaded the VMTK
>     from thier website, but I have no idea how to make the two work
>     with one another. I am struggling to understand the instructions
>     in the Wiki forum (since I have no experience with computer
>     programs like this). I have approached the computer science
>     department and they are also unsure.
>
>     I apologise for the inconvenience and realise you are very busy.
>     I would appreciate any help you can give me.
>
>     Sincerely
>     Anica
>
>     Sent from my iPad

     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.



--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


_______________________________________________
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.



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: Fwd: Re: VMTK Slicer4 problem?

Jean-Christophe Fillion-Robin


On Wed, May 14, 2014 at 7:27 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:


On Wed, May 14, 2014 at 7:24 AM, Steve Pieper <[hidden email]> wrote:
Looks like there was a build error on the vmtk extension last night, so it'll take another round of debugging before it's in the nightly.  Sorry for the delay.

-Steve


On Wed, May 14, 2014 at 2:30 AM, Madan Rao <[hidden email]> wrote:
Hi,

Daniel Haehn has developed VMTK module for Slicer as an application for coronary arteries.Therefore, VMTK was standardized for coronaries and lot of online information is available (some links below). I assume you need to work on coronaries first and get a first hand experience before you venture with cerebral arteries.



AM Mohan Rao


On Wed, Apr 16, 2014 at 6:17 PM, Ron Kikinis <[hidden email]> wrote:
Hi,

I have added the slicer user mailing list, since this is of potential
general interest. We had a version of vmtk integrated with slicer in an
earlier version of Slicer. We are in the process of porting to the
current version of Slicer.

1. Search for vmtk in the following page:
http://www.slicer.org/slicerWiki/index.php/Documentation-3.6
2. To download 3.6: http://www.slicer.org/pages/Special:SlicerDownloads

Ron




-------- Original Message --------
Subject:        Re: VMTK Slicer4 problem?
Date:   Wed, 16 Apr 2014 08:38:19 -0400
From:   Steve Pieper <[hidden email]>


Hi Ron -

I believe we are "close" to a solution - the VMTK extension works great
on local builds, and Jc knows how to fix the extension loading issues
that have stumped the rest of us for a couple years now.  @Jc can you
give an update on that?

-Steve


On Wed, Apr 16, 2014 at 8:19 AM, Ron Kikinis <[hidden email]
<mailto:[hidden email]>> wrote:



     Sent from my mobile phone.

     Begin forwarded message:

>     *Date:* April 16, 2014 at 1:30:27 AM MDT
...
>     *To:* "[hidden email] <mailto:[hidden email]>"
>     <[hidden email] <mailto:[hidden email]>>
>     *Subject:* *VMTK Slicer4 problem?*
>
>     Dear Dr Ron Kikinis
>
....

>     I am busy conducting my research on hemispheric lateralisation and
>     its relationship with asymmetry of the carotid arteries. The
>     supervisor for my thesis is Professor Mark Solms (head of the
>     Psychology Department).
>     I really want to use Slicer4 3D with the vascular modeling toolkit
>     for the geometric analysis of my thesis, but I am really
>     struggling to make it work. My DICOM database consists of CTAngios
>     of the head and neck ( and I have Windows 64-bit laptop).
>     I have downloaded the slicer program, and have downloaded the VMTK
>     from thier website, but I have no idea how to make the two work
>     with one another. I am struggling to understand the instructions
>     in the Wiki forum (since I have no experience with computer
>     programs like this). I have approached the computer science
>     department and they are also unsure.
>
>     I apologise for the inconvenience and realise you are very busy.
>     I would appreciate any help you can give me.
>
>     Sincerely
>     Anica
>
>     Sent from my iPad

     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.



--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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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: Fwd: Re: VMTK Slicer4 problem?

Attila Nagy
Wow!

Thank you very much guys for being this quick!
We'll definitely give it a try and see how the extension works on our data. The original idea is about segmenting extracranial vessels so ours might very well be a special case - but at l least we can try it now :))

Thanks again!
Attla

--------------------------------------------
14. 5. 15, Csüt. napon Jean-Christophe Fillion-Robin <[hidden email]> ezt írta:

 Tárgy: Re: [slicer-users] Fwd: Re: VMTK Slicer4 problem?
 Címzett:: "Steve Pieper" <[hidden email]>
 Másolat: "[hidden email]" <[hidden email]>
 Dátum: 2014. május. 15., Csütörtök, 20:50
 
 And based on
 today's the dashboard, I fixed the remaining of the
 issues ...
 
 For details:
   http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23181
 
 
   https://github.com/vmtk/SlicerExtension-VMTK/commit/f5b79887b2dc00b18b06e4299256916f3c188578
 
 
 
 
 On Wed, May 14, 2014
 at 7:27 PM, Jean-Christophe Fillion-Robin <[hidden email]>
 wrote:
 
 
 Hi Folks,
 
 I just fixed this issue. Tomorrow nightly should be
 better.
 
 
 
 For details:
   http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23180
 
   https://github.com/vmtk/SlicerExtension-VMTK/commit/93634d059fa82c4ca3b6f523ab6fdc84770445eb
 
 
 
 Thanks
 
 Jc
 
 
 On Wed, May 14, 2014
 at 7:24 AM, Steve Pieper <[hidden email]>
 wrote:
 
 
 
 Looks like there was a build error on the vmtk
 extension last night, so it'll take another round of
 debugging before it's in the nightly.  Sorry for the
 delay.
 
 
 
 -Steve
 
 
 On Wed, May 14, 2014
 at 2:30 AM, Madan Rao <[hidden email]>
 wrote:
 
 
 
 
 Hi,
 Daniel Haehn has developed VMTK module for Slicer
 as an application for coronary arteries.Therefore, VMTK was
 standardized for coronaries and lot of online information is
 available (some links below). I assume you need to work on
 coronaries first and get a first hand experience before you
 venture with cerebral arteries.
 
 
 
 
 
 http://www.slicer.org/slicerWiki/index.php/Modules:VMTK_in_3D_Slicer_Tutorial:_Coronary_Artery_Centerline_Extraction
 
 
 
 
 
 
 https://www.slicer.org/slicerWeb/images/6/62/Christopher-CardSoc2011.pdf
 
 
 
 
 
 AM Mohan Rao
 
 
 On Wed, Apr 16, 2014
 at 6:17 PM, Ron Kikinis <[hidden email]>
 wrote:
 
 
 
 
 
 Hi,
 
 
 
 I have added the slicer user mailing list, since this is of
 potential
 
 general interest. We had a version of vmtk integrated with
 slicer in an
 
 earlier version of Slicer. We are in the process of porting
 to the
 
 current version of Slicer.
 
 
 
 1. Search for vmtk in the following page:
 
 http://www.slicer.org/slicerWiki/index.php/Documentation-3.6
 
 2. To download 3.6: http://www.slicer.org/pages/Special:SlicerDownloads
 
 
 
 Ron
 
 
 
 
 
 
 
 
 
 -------- Original Message --------
 
 Subject:        Re: VMTK Slicer4 problem?
 
 Date:   Wed, 16 Apr 2014 08:38:19 -0400
 
 From:   Steve Pieper <[hidden email]>
 
 
 
 
 
 Hi Ron -
 
 
 
 I believe we are "close" to a solution - the VMTK
 extension works great
 
 on local builds, and Jc knows how to fix the extension
 loading issues
 
 that have stumped the rest of us for a couple years now.
  @Jc can you
 
 give an update on that?
 
 
 
 -Steve
 
 
 
 
 
 On Wed, Apr 16, 2014 at 8:19 AM, Ron Kikinis <[hidden email]
 
 <mailto:[hidden email]>>
 wrote:
 
 
 
 
 
 
 
      Sent from my mobile phone.
 
 
 
      Begin forwarded message:
 
 
 
 >     *Date:* April 16, 2014 at 1:30:27 AM MDT
 
 ...
 
 >     *To:* "[hidden email]
 <mailto:[hidden email]>"
 
 >     <[hidden email]
 <mailto:[hidden email]>>
 
 >     *Subject:* *VMTK Slicer4 problem?*
 
 >
 
 >     Dear Dr Ron Kikinis
 
 >
 
 ....
 
 
 
 >     I am busy conducting my research on hemispheric
 lateralisation and
 
 >     its relationship with asymmetry of the carotid
 arteries. The
 
 >     supervisor for my thesis is Professor Mark Solms
 (head of the
 
 >     Psychology Department).
 
 >     I really want to use Slicer4 3D with the vascular
 modeling toolkit
 
 >     for the geometric analysis of my thesis, but I am
 really
 
 >     struggling to make it work. My DICOM database
 consists of CTAngios
 
 >     of the head and neck ( and I have Windows 64-bit
 laptop).
 
 >     I have downloaded the slicer program, and have
 downloaded the VMTK
 
 >     from thier website, but I have no idea how to
 make the two work
 
 >     with one another. I am struggling to understand
 the instructions
 
 >     in the Wiki forum (since I have no experience
 with computer
 
 >     programs like this). I have approached the
 computer science
 
 >     department and they are also unsure.
 
 >
 
 >     I apologise for the inconvenience and realise you
 are very busy.
 
 >     I would appreciate any help you can give me.
 
 >
 
 >     Sincerely
 
 >     Anica
 
 >
 
 >     Sent from my iPad
 
 
 
      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.
 
 
 
 
 
 
 
 --
 
 Ron Kikinis, M.D.,
 
 Robert Greenes Distinguished Director of Biomedical
 Informatics
 
 Professor of Radiology, Harvard Medical School
 
 Director, Surgical Planning Laboratory
 
 http://www.spl.harvard.edu/~kikinis
 
 
 
 
 
 _______________________________________________
 
 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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 [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.
 
 
 
 
 
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 To unsubscribe: send email to [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
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 contains patient information, please contact the Partners
 Compliance HelpLine at
 
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 . If the e-mail was sent to you in error
 
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 --
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