Hello FreeSurfer Developers,

I'm attempting to compute cortical thickness and to analyze it between groups.

So I perform "recon-all", but rather than using recon-all -all, some problems arise while performing each of the steps in it. These problems are as follwing.

1. -whitesurf process is preceded over smooth2 and inflated2 in recon-all file, really it is not. why?

2. This error first started during -cortribbon process, also occurs in other processes such as -cortparc2, -cortparc3, -hyporelabel, -aparc2aseg, and -wmparc. But these process does not ask for a file called aseg as input if you check it on the homepage. Can you tell me how to fix it?

error: mghRead(/media/hwang/Disk1/cp2ANZ/FREESURFER/mri/aseg.mgz, -1): could not open file

error: cannot compute vol stats without /media/hwang/Disk1/cp2ANZ/FREESURFER/mri/aseg.mgz

Command exited with non-zero status 1

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
2) Platform: Ubuntu release 18.04.1
3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

Thank you very much.

Sincerely,

Yoonho

Hwang, Yoonho

Medical Image Processing Laboratory (MIPL),

Department of Biomedical Engineering, Yonsei University.

#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,

Gangwon-do, 26493, Republic of Korea.

Office: +82-33-760-2499

Email: ken.lmstar11@gmail.com