I see the CLUT file, it's the same one I've been using. I have been using FSL (fslmaths) to extract anatomical ROIs from the aparc+aseg using the CLUT indices as thresholds. This normally works, but results in empty ROIs for thalamic nuclei (but not for whole thalamus). What do you think could be the problem?

Best,

Ameen

On Fri, Jul 17, 2020 at 10:33 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

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

External Email - Use Caution

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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Ameen Al Qadi

MSBS Candidate

Icahn School Of Medicine at Mount Sinai '20

+1-646-500-1521

ameen.alqadi@icahn.mssm.edu