load a FS surface label into 3D slicer

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load a FS surface label into 3D slicer

Prapti Gautam

 

Hi,

 

I am trying to load a custom-made FreeSurfer surface label in Slicer 3D as a volume file, but have not been able to do so satisfactorily. I have created a label file in the format of both .label and .annot .. Has anyone encountered this problem before and has found a solution for it ?

 

Thanks,

 

 

Prapti

 

 


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Re: load a FS surface label into 3D slicer

swallace
Hi Prapti-

We have a 3D visualization of Freesurfer data module and tutorial on the
slicer web page. Give that a look and let us know if you have any
problems.

Stuart

>
>
> Hi,
>
>
>
> I am trying to load a custom-made FreeSurfer surface label in Slicer 3D
> as a volume file, but have not been able to do so satisfactorily. I have
> created a label file in the format of both .label and .annot .. Has
> anyone encountered this problem before and has found a solution for it ?
>
>
>
> Thanks,
>
>
>
>
>
> Prapti
>
>
>
>
>
> _______________________________________________
> 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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slicer.org down?

swallace
In reply to this post by Prapti Gautam
Hi all,

Anyone else having issues getting onto the slicer/org site? I'm able to
get to the home page, but upon clicking on any other link (tutorials,
documentation, etc), it hangs/times out.

Stuart
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Re: load a FS surface label into 3D slicer

Prapti Gautam
In reply to this post by swallace
Hi

Yes, I've looked at the visualisation tutorial and that has been very
helpful, but it doesn't cover what one would do with a custom label as
it cannot be loaded as a volume or a model/scene file. I was just
wondering if anyone else has encountered this problem before,

Thanks,

Prapti

 
-----Original Message-----
From: [hidden email] [mailto:[hidden email]]

Sent: Tuesday, 25 May 2010 12:57 PM
To: Prapti Gautam
Cc: [hidden email]
Subject: Re: [slicer-users] load a FS surface label into 3D slicer

Hi Prapti-

We have a 3D visualization of Freesurfer data module and tutorial on the
slicer web page. Give that a look and let us know if you have any
problems.

Stuart

>
>
> Hi,
>
>
>
> I am trying to load a custom-made FreeSurfer surface label in Slicer
3D
> as a volume file, but have not been able to do so satisfactorily. I
have
> created a label file in the format of both .label and .annot .. Has
> anyone encountered this problem before and has found a solution for it
?

>
>
>
> Thanks,
>
>
>
>
>
> Prapti
>
>
>
>
>
> _______________________________________________
> 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: load a FS surface label into 3D slicer

swallace
If you're trying to load it as a volume, you will probably want it as a
.mgz file. Have you tried using the Freesurfer command mri_label2vol? It's
output can be .mgz:

http://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2vol

Stuart


> Hi
>
> Yes, I've looked at the visualisation tutorial and that has been very
> helpful, but it doesn't cover what one would do with a custom label as
> it cannot be loaded as a volume or a model/scene file. I was just
> wondering if anyone else has encountered this problem before,
>
> Thanks,
>
> Prapti
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]]
>
> Sent: Tuesday, 25 May 2010 12:57 PM
> To: Prapti Gautam
> Cc: [hidden email]
> Subject: Re: [slicer-users] load a FS surface label into 3D slicer
>
> Hi Prapti-
>
> We have a 3D visualization of Freesurfer data module and tutorial on the
> slicer web page. Give that a look and let us know if you have any
> problems.
>
> Stuart
>
>>
>>
>> Hi,
>>
>>
>>
>> I am trying to load a custom-made FreeSurfer surface label in Slicer
> 3D
>> as a volume file, but have not been able to do so satisfactorily. I
> have
>> created a label file in the format of both .label and .annot .. Has
>> anyone encountered this problem before and has found a solution for it
> ?
>>
>>
>>
>> Thanks,
>>
>>
>>
>>
>>
>> Prapti
>>
>>
>>
>>
>>
>> _______________________________________________
>> 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: load a FS surface label into 3D slicer

Aucoin, Nicole
In reply to this post by Prapti Gautam
Slicer can load surface geometry in the .curv and .w FreeSurfer formats
through the Add Model functionality. Once the base geometry is read in,
you can add a scalar overlay to a selected model using the Add Scalar
Overlay functionality (assuming that the scalar overlay matches up value
to vertex with the model geometry). These scalar overlays can be in
.label, .annot, .mgz format (the last being the volume format).
But we don't support just reading in a surface label file on it's own,
it has to be associated with a geometry file.

Nicole


Prapti Gautam wrote:

>
>  
>
> Hi,
>
>  
>
> I am trying to load a custom-made FreeSurfer surface label in Slicer
> 3D as a volume file, but have not been able to do so satisfactorily. I
> have created a label file in the format of both .label and .annot ..
> Has anyone encountered this problem before and has found a solution
> for it ?
>
>  
>
> Thanks,
>
>  
>
>  
>
> Prapti
>
>  
>
>  
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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: load a FS surface label into 3D slicer

Prapti Gautam
Great thank you, that solved the problem,

Prapti

 
-----Original Message-----
From: Nicole Aucoin [mailto:[hidden email]]
Sent: Wednesday, 26 May 2010 1:48 AM
To: Prapti Gautam
Cc: [hidden email]
Subject: Re: [slicer-users] load a FS surface label into 3D slicer

Slicer can load surface geometry in the .curv and .w FreeSurfer formats
through the Add Model functionality. Once the base geometry is read in,
you can add a scalar overlay to a selected model using the Add Scalar
Overlay functionality (assuming that the scalar overlay matches up value

to vertex with the model geometry). These scalar overlays can be in
.label, .annot, .mgz format (the last being the volume format).
But we don't support just reading in a surface label file on it's own,
it has to be associated with a geometry file.

Nicole


Prapti Gautam wrote:
>
>  
>
> Hi,
>
>  
>
> I am trying to load a custom-made FreeSurfer surface label in Slicer
> 3D as a volume file, but have not been able to do so satisfactorily. I

> have created a label file in the format of both .label and .annot ..
> Has anyone encountered this problem before and has found a solution
> for it ?
>
>  
>
> Thanks,
>
>  
>
>  
>
> Prapti
>
>  
>
>  
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> 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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