I don't know. I'm not that familiar with FSL programs. If you want our help, try using mri_segstats. If something goes wrong send the command line
On 7/21/2020 10:26 AM, Al Qadi, Ameen wrote:
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Hi Douglas,
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 mailto: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 <mailto:ameen.alqadi@icahn.mssm.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@icahn.mssm.edu mailto:ameen.alqadi@icahn.mssm.edu -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@icahn.mssm.edu mailto:ameen.alqadi@icahn.mssm.edu