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For the sclimbic, you can find it in $FREESURFER/models/sclimbic.ctab
For the brainstem, the labels are in the main FS table, $FREESURFER/FreeSurferColorLUT.txt
I think there are only three labels in the brainstem, so you can load it into freeview to pull out the indices


On 5/22/2023 9:18 AM, Yoo, Chi-Hyeon wrote:

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Hello, 

 

I am Chi-Hyeon, a postdoc at the Martinos Center. 

 

One of my colleagues wants to try to use advance segmentations: brainstem substructures segmentation (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures), and limbic segmentation (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic). 

 

Thanks to the instructions, I was able to generate the segmentations but I cannot find the lookup table for the labels for this versions of segmentation. 

I will need a look-up table to generate binary masks from these segmentations to eventually export PET values from that binary segmentation masks. 

Please let me know where I could find the labels for these sets of segmentations. 

 

Chi-Hyeon

 

 


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