Sorry, I see the error in the log now.
Can you check if
1. you have fsaverage symbolic link created in your SUBJECTS_DIR /scratch/junhong.yu/COBRE/output/sourcedata/Freesurfer/fsaverage
2. BA1_exvivo Labels exist in /usr/local/freesurfer-7.2.0/subjects/fsaverage/label/*BA1_exvivo*
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Huang, Yujing
Sent: Wednesday, January 11, 2023 9:11 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
Hi Junhong,
I don’t see the error in your attached recon-all.log. It seems like you are running recon-all in stages. Attached is your autorecon1 log.
For 7.3.2 autorecon2, append '-careg' to your command line should works.
Best,
Yujing
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Yu Junhong (Dr)
Sent: Wednesday, January 11, 2023 4:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
External Email - Use Caution
Hi there,
I’ve been trying run recon-all on this public dataset
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://link.springer.com/article/10.1007/s12021-017-9338-9 and I cant seem to complete the autorecon3 stage for any of the
subjects. I’ve attached the log file.
I’m using freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
#--------------------------------------------
#@# BA_exvivo Labels lh Mon Jan 9 05:39:18 +08 2023
-------------------------------------------------------------------------
ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage!
The fsaverage link probably points to an older freesurfer version
-------------------------------------------------------------------------
Linux hpc-gekko1 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-A00000300 exited with ERRORS at Mon Jan 9 05:39:18 +08 2023
I’ve also tried to recon-all with freesurfer 7.3.2. however I got stuck at the autorecon2 stage instead
ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform
I’m wondering if there is anything wrong with the data?
The input file can be downloaded here
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1us8Oe6NH5DedbajaE0LwFqb58jwxBJU2/view?usp=sharing
Thanks
Junhong
CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it,
notify us and do not copy, use, or disclose its contents.
Towards a sustainable earth: Print only when necessary. Thank you.