On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:

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Dear Freesurfer Developers,

I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer:

Is there a new CLUT associated with FS7? I tried to use the CLUT labels to extract thalamic subnuclei ROIs, but got empty ROI files.

They should be in $FREESURFER/FreeSurferColorLUT.txt
How are you extracting?

Given that Freesurfer version 7 contains segmentations not previously generated in recon-all (i.e. hippocampal subfields), is it possible to extract these ROIs using aparc+aseg images generated using previous versions of Freesurfer? Or do we need to repeat the cortical parcellations (i.e. rerun recon-all) using FS7?

You can run the hippocamal and thalamic segs on FS version 6 subjects.

I’d highly appreciate your time and feedback on this matter. Thank you.

Best,

Ameen
--

Ameen Al Qadi
MSBS Candidate

Icahn School Of Medicine at Mount Sinai '20

+1-646-500-1521

ameen.alqadi@icahn.mssm.edu
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