Hi Eugenio,

Thank you for your reply.  Somehow the display from my thalamic segmentation does not capture the colors in your publication and furthermore, the nuclei are not clearly delineated from each other visually since one color may encompass two or three different nuclei.  However, I see the label numbers ranging from 8100 to 8300 when hovering my mouse over the segmented thalamus and also these numbers change within the same color meaning that delineation does in fact exist; these new label numbers are different from the 14 FreeSurferColorLut.txt thalamic labels.  Is there a table that links these new label numbers with the names of the 26 thalamic nuclei?

Thanks again for your help,

Vinny

On Mon, Sep 10, 2018 at 1:36 PM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

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Hi Vinny,

The anatomical definitions can be found in the paper, which is open access (see Table 2):

https://www.sciencedirect.com/science/article/pii/S1053811918307109

Kind regards

Eugenio

Sent from my phone, please excuse brevity and typos

From: Vinny K

Sent: Monday, September 10, 10:35

Subject: Re: [Freesurfer] thalamic segmentation

To: freesurfer@nmr.mgh.harvard.edu

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Hi,

I ran recon-all to generate the required files for the thalamic segmentation tool (http://freesurfer.net/fswiki/ThalamicNuclei) using the latest development version of Freesurfer (06/09/2018) linux-cent06.  The segmented thalamic nuclei were visualized but I could not find a table listing the thalamic nuclei and its associated label to help identify the specific nuclei.

Any help would be greatly appreciated.

Thanks,

Vinny

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