thalamic segmentation

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thalamic segmentation

Jonathan DuBois-2
Hi, 

I noticed on the slicer training page that there is an example of merging the A0 atlas with segmentation of thalamic nuclei with the A1 atlas. However the training for segmentation with Slicer only segments grey, white, csf, skull, ect. Our raw data is in dicom format, and is processed with Freesurfer in mgz format. Is there a way to process this data through slicer for segmentation of thalamic nuclei? 

Thank you

Jonathan DuBois


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Re: thalamic segmentation

swallace
Hiya Jonathan,

We have a tutorial on visualization of Freesurfer data here (just FYI):

http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training

Are you starting from raw dicom/mgz and are looking for an automated
thalamus segmentation within Slicer?

Stuart



> Hi,
>
> I noticed on the slicer training page that there is an example of merging
> the A0 atlas with segmentation of thalamic nuclei with the A1 atlas.
> However
> the training for segmentation with Slicer only segments grey, white, csf,
> skull, ect. Our raw data is in dicom format, and is processed with
> Freesurfer in mgz format. Is there a way to process this data through
> slicer
> for segmentation of thalamic nuclei?
>
> Thank you
>
> Jonathan DuBois
> _______________________________________________
> 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: thalamic segmentation

Jonathan DuBois-2
Yes, I was wondering if it was possible to process dicom or freesurfer/mgz (our data has been fully processed with freesurfer, although we have raw dicoms as well) with Slicer to get segmentation of the thalamic nuclei? And if there was a tutorial available to do so?

Jon



On Tue, Jun 1, 2010 at 4:16 PM, <[hidden email]> wrote:
Hiya Jonathan,

We have a tutorial on visualization of Freesurfer data here (just FYI):

http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training

Are you starting from raw dicom/mgz and are looking for an automated
thalamus segmentation within Slicer?

Stuart



> Hi,
>
> I noticed on the slicer training page that there is an example of merging
> the A0 atlas with segmentation of thalamic nuclei with the A1 atlas.
> However
> the training for segmentation with Slicer only segments grey, white, csf,
> skull, ect. Our raw data is in dicom format, and is processed with
> Freesurfer in mgz format. Is there a way to process this data through
> slicer
> for segmentation of thalamic nuclei?
>
> Thank you
>
> Jonathan DuBois
> _______________________________________________
> 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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