External Email - Use Caution
Dear FreeSurfer Developers,
I’m trying to run recon-all as a pre-processing step in the AFNI resting-state analysis pipline, using the command: recon-all -subject $subj -i $anat_cm -all -parallel
So far it has successfully run on about 20 participants in my sample, but for the current participant it’s now suddenly throwing this error:
PIDs (691564 691567) completed and logs appended. Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s R21-24 exited with ERRORS at Fri Apr 5 16:29:23 EDT 2024
I searched through the log file, tried Googling the error, and searched your email list archive, but couldn’t find anything to address this. The log file is attached, along with:
1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.3 LTS
I’d appreciate any help or advice you could give!
Best, Will
--- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://secure-web.cisco.com/1j9r5gk2jDdMnViAisDWP_vqMXxEmt7r1AWEWqCgjw6_9jXD...
It looks like mris_fix_topology for lh hemisphere core dumped. This is from your recon-all.log:
“ An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... Large defect found - not a problem, but a curiousity *** stack smashing detected ***: terminated “
In the tutorial, it has instructions on how to correct topological defects.
Also, I noticed that the recon-all was run with ‘-parallel’ option. Use ‘-nthreads <num-of-threads>’ instead.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of William Graves Sent: Sunday, April 7, 2024 10:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all exits with errors
External Email - Use Caution Dear FreeSurfer Developers,
I’m trying to run recon-all as a pre-processing step in the AFNI resting-state analysis pipline, using the command: recon-all -subject $subj -i $anat_cm -all -parallel
So far it has successfully run on about 20 participants in my sample, but for the current participant it’s now suddenly throwing this error:
PIDs (691564 691567) completed and logs appended. Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s R21-24 exited with ERRORS at Fri Apr 5 16:29:23 EDT 2024
I searched through the log file, tried Googling the error, and searched your email list archive, but couldn’t find anything to address this. The log file is attached, along with:
1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.3 LTS
I’d appreciate any help or advice you could give!
Best, Will
--- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://lbbil.rutgers.edu
External Email - Use Caution
That worked beautifully. Thank you Yujing!
Best, Will
On Apr 8, 2024, at 8:58 AM, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
It looks like mris_fix_topology for lh hemisphere core dumped. This is from your recon-all.log:
“ An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://secure-web.cisco.com/1AL1TsrfyQOUqCIXXBqx1RFKat7TzQnns9gtsP_SH6wzu0J... Large defect found - not a problem, but a curiousity *** stack smashing detected ***: terminated “
In the tutorial, it has instructions on how to correct topological defects.
Also, I noticed that the recon-all was run with ‘-parallel’ option. Use ‘-nthreads <num-of-threads>’ instead.
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 William Graves Sent: Sunday, April 7, 2024 10:03 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all exits with errors
External Email - Use Caution
Dear FreeSurfer Developers,
I’m trying to run recon-all as a pre-processing step in the AFNI resting-state analysis pipline, using the command: recon-all -subject $subj -i $anat_cm -all -parallel
So far it has successfully run on about 20 participants in my sample, but for the current participant it’s now suddenly throwing this error:
PIDs (691564 691567) completed and logs appended. Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s R21-24 exited with ERRORS at Fri Apr 5 16:29:23 EDT 2024
I searched through the log file, tried Googling the error, and searched your email list archive, but couldn’t find anything to address this. The log file is attached, along with:
1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.3 LTS
I’d appreciate any help or advice you could give!
Best, Will
--- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://secure-web.cisco.com/1JFnzsz1va8MJlbUd3wgkrsTxdVUt375K3mHIHN6XQL6fWR6...http://secure-web.cisco.com/1ub3N-gye177rpuctWMW0Qh4jFHS6ARn7_EpqhMneXWx4bqBInrTbuHiOHqzs_DhJ5WVraQc6fFNDjhC6SFAGAOeQXkUABDiZ5cKn5Nf2ib-uXf3PW0HYIJA8nxaLiozqbVsaDbfD2KsucmwyJLoHKurYqbXxII_-cCujfJY3gkByGVCjrzzMt6fnjZK__2cvCG_QIsgxu6WEscd8_9YgSKH-PaS64LZ67NHwDlqreo5dXKXiMa9VMn5RDqay6LKb5ebAKFQj8-Va6SpBnGyNlexfk7zQ21hzAkTRP782Tsrfk-QmkSl-uOG5zDZINXHDSa8P_YFZmZC1LFYwjxaBRw/http%3A%2F%2Flbbil.rutgers.edu%2F _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Nk-5NeFOrDTjmmdys3LmERUUspIT3zSLEhkBf-HbgY4U2z... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1nbPAfcfHKQx971pUD4AmKNEg5jeUR_DNDoyN5mengH80Sp... https://secure-web.cisco.com/1nbPAfcfHKQx971pUD4AmKNEg5jeUR_DNDoyN5mengH80SpAG9uMsVE_pOtcPrILGQEUrqvp5iUf_AQtlXRUE4X3jJa1ivpEzbDuKV8x-HrVpJGjmPJtwieYG9862xhxt6E4eCdeEE0S89oBE7jcrPQAhzDsEpdJyAoR_aM1gqQ8mEZhgZrFbKzQPS5EZz5lijGvQOP-v9D1qvHE0fwAX0puzlmVnrqeBF7C3apzXsQPQqfCW5Jnq3VPi3T2IrOryQQF4ATRMCCZykW8FPZ6kai653HR94mdq01UKd_ChCWTr-egPOErmwp18ycJorD_jBxeHZNT7uQD8bR93dtSiNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
William Graves