1. You can use mri_segstats (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats) to generate the missing stats/aseg.stats. 2. 'colortable_BA_thresh.txt' is not intended for FS 7.4.0 or 7.4.1. Your fix of colortable_BA_thresh.txt is fine. 3. Here https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical you can find the announcement of bug fixes.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Biondo, Francesca Sent: Tuesday, November 14, 2023 6:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon_all_clinical and aseg.stat

External Email - Use Caution

Hello! I encountered 3 issues with recon_all_clinical:

1. Both version 7.4.0 and version 7.4.1 do not generate aseg.stat file. Is this normal? I would like to extract volume parcellations via asegstats2table given that I need the volume parcellations as typically presented in aseg.stat. Is there a way to extract aseg.stat from aseg.mgz or another solution to extract aseg.stat volumes? 2. Version 7.4.0 throws errors at the end of the script (even with the replacement file). "ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt" and "ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt." I checked, "colortable_BA.txt" exists but "colortable_BA_thresh.txt" doesn't. If I rename the latter file to "colortable_BA_thresh.txt", then it fixes the errors. Is this the correct way to address the problem? 3. Version 7.4.1 has a similar error as above, but it seems to be due to the incorrect path: ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt. Any help, particularly with problem 1, would be much appreciated! Thank you, Fran

Francesca Biondo, PhD | Senior Research Fellow | Centre for Medical Image Computing | Computer Science | UCL | f.biondo@ucl.ac.ukmailto:f.biondo@ucl.ac.uk