External Email - Use Caution
Hi there,
I’ve been trying run recon-all on this public dataset https://secure-web.cisco.com/13AIuH-XEB3a4SQgLqeatTFX2txFlVseSmTdhYjjSnmJ3KG... 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 https://secure-web.cisco.com/1kuOf_Y-BPoVdkGgGQL_IV4l7nF5eQ5cy4kb3Lu9CxxDEaZ...
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.
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/s12021-017-9338-9https://secure-web.cisco.com/13AIuH-XEB3a4SQgLqeatTFX2txFlVseSmTdhYjjSnmJ3KGHiZfnrz9gItbIUs3PsBWKAVQo3qvvtJ8WJBaRlndzV0DNIPSxTTJ60TVgZ00HE8lVZeE6AO3jg9vbAScVG94lgngU2SwQupaftOjhbBQXM04xq4-vnqgNGb219_Iv1TrFOpL_wquFsNIk96S9zcP5sdDNgPf0r0RagA6_eCKrhs-gUqPy8vvO16stnx6UfNH581uh8aHjheCcmv6ZZ2YqG5P4fbZUvxKdL7k0ehm8IpfXwWN9-FXsMRYcXT4lVEDL_zptxxiM07hAcVpEu0v5Yal0FCRNgw5huicOvUQ/https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs12021-017-9338-9 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=s...https://secure-web.cisco.com/1kuOf_Y-BPoVdkGgGQL_IV4l7nF5eQ5cy4kb3Lu9CxxDEaZe2YBFAnAXZCDLkYc3XKaxzF2VooMxmEngav0PcRzICH1Yrzg7Tfzt2kZumAHzWz6VUEuiUNClfBhEV-BOUmeFAqsSJZ7bZ-54micbH7X1RblOYN18tXwtNQSX-12ZUSTA5vSncNPlglKeRxXSlYoU_i-TV8VV6_rjOBVMq_8ZSKTGYijK0ai2Zwijtrvt1wportHbF-7YQJjF7g9zc5ZFMvNPQd-YxOKyGcnISUKuX-vkldOUar9nJJEr8ZGSqmC_CVhNIN3p2QD6sH637ztowAAHS88RsAMbBH1mlNw/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1us8Oe6NH5DedbajaE0LwFqb58jwxBJU2%2Fview%3Fusp%3Dsharing
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.
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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/s12021-017-9338-9https://secure-web.cisco.com/13AIuH-XEB3a4SQgLqeatTFX2txFlVseSmTdhYjjSnmJ3KGHiZfnrz9gItbIUs3PsBWKAVQo3qvvtJ8WJBaRlndzV0DNIPSxTTJ60TVgZ00HE8lVZeE6AO3jg9vbAScVG94lgngU2SwQupaftOjhbBQXM04xq4-vnqgNGb219_Iv1TrFOpL_wquFsNIk96S9zcP5sdDNgPf0r0RagA6_eCKrhs-gUqPy8vvO16stnx6UfNH581uh8aHjheCcmv6ZZ2YqG5P4fbZUvxKdL7k0ehm8IpfXwWN9-FXsMRYcXT4lVEDL_zptxxiM07hAcVpEu0v5Yal0FCRNgw5huicOvUQ/https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs12021-017-9338-9 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=s...https://secure-web.cisco.com/1kuOf_Y-BPoVdkGgGQL_IV4l7nF5eQ5cy4kb3Lu9CxxDEaZe2YBFAnAXZCDLkYc3XKaxzF2VooMxmEngav0PcRzICH1Yrzg7Tfzt2kZumAHzWz6VUEuiUNClfBhEV-BOUmeFAqsSJZ7bZ-54micbH7X1RblOYN18tXwtNQSX-12ZUSTA5vSncNPlglKeRxXSlYoU_i-TV8VV6_rjOBVMq_8ZSKTGYijK0ai2Zwijtrvt1wportHbF-7YQJjF7g9zc5ZFMvNPQd-YxOKyGcnISUKuX-vkldOUar9nJJEr8ZGSqmC_CVhNIN3p2QD6sH637ztowAAHS88RsAMbBH1mlNw/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1us8Oe6NH5DedbajaE0LwFqb58jwxBJU2%2Fview%3Fusp%3Dsharing
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.
freesurfer@nmr.mgh.harvard.edu
-
Huang, Yujing -
Yu Junhong (Dr)