External Email - Use Caution
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. By perform "Curvature Stats" of recon-all in parallel, This process is required for ?h.curv file. This file is created after -white or -whitesurf process, but looking at recon-all file in /usr/local/freesurfer/bin/, -whitesurf is running after this process, so I think so, Is it correct to move position of curvature stats after the pialsurf to fix the error?*
*2. Looking at https://secure-web.cisco.com/1GkMeZvnVnQ05ojl-46PZk8Ur4cuLzS11EOrMEhAlenwlbU... https://secure-web.cisco.com/1GkMeZvnVnQ05ojl-46PZk8Ur4cuLzS11EOrMEhAlenwlbUny-kZmDWjcyVx-ZcTA5SoQ6sEl5NtEzSC_FXto40aFIA0GOzmTqQfZX8gOc5mNg25PWi9Lux1Jcqv6JxnyDHzL_fVXyjzknbCfGS7juCgEcVbikW_ZRJtl0rFZSSo6Qdo5OtLf4coYUOH2rFGX1vhlPnU84VeOk-GnD4XISgM_nAirDwb6d8YkQf-ekkFCKNLgvktMmDurMhZvlP3Qh5udxt-4fxvABhbeIHwXAw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable and recon-all file, because order of autorecon -all is different between two reference, I am confused. Can you please tell me which one to refer to?*
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
Yes, this is a known error that will be fixed in 7.2, thanks for pointing it out
On 4/9/2021 2:51 AM, Yoonho Hwang wrote:
External Email - Use Caution
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. By perform "Curvature Stats" of recon-all in parallel, This process is required for ?h.curv file. This file is created after -white or -whitesurf process, but looking at recon-all file in /usr/local/freesurfer/bin/, -whitesurf is running after this process, so I think so, Is it correct to move position of curvature stats after the pialsurf to fix the error?*
*2. Looking at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable https://secure-web.cisco.com/1GkMeZvnVnQ05ojl-46PZk8Ur4cuLzS11EOrMEhAlenwlbUny-kZmDWjcyVx-ZcTA5SoQ6sEl5NtEzSC_FXto40aFIA0GOzmTqQfZX8gOc5mNg25PWi9Lux1Jcqv6JxnyDHzL_fVXyjzknbCfGS7juCgEcVbikW_ZRJtl0rFZSSo6Qdo5OtLf4coYUOH2rFGX1vhlPnU84VeOk-GnD4XISgM_nAirDwb6d8YkQf-ekkFCKNLgvktMmDurMhZvlP3Qh5udxt-4fxvABhbeIHwXAw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable and recon-all file, because order of autorecon -all is different between two reference, I am confused. Can you please tell me which one to refer to?*
- 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 mailto:ken.lmstar11@gmail.com*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Yoonho Hwang