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Please list: > version of freersurfer you are running> OS name and version you are running> amount of RAM on your machine - R. On Feb 20, 2025, at 05:58, Brunno M. de Campos <brunno@unicamp.br> wrote: External Email - Use Caution Dear all,I run my script for longitudinal processing based on: individual processing (recon-all -i) + base image creation (recon-all -base) and longitudinal processing (recon-all -long).In some cases (not always), the process terminates with errors, apparently at the same stage. The log states, among other things, "Reading texture...*** buffer overflow detected ***: terminated Command terminated by signal 6".1 - I assume that I have exceeded my memory capacity. Am I correct? I have, in fact, written a script that parallelizes these processes, but I might be distributing the workload poorly if that is the case.2 - If this is indeed the issue, do you know the peak memory required for such a process?Thank you!Brunno M Campos University of Campinas
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Hi, thanks.
version of freersurfer you are running: 7.4.1 OS name and version you are running: Ubuntu 22 amount of RAM on your machine: 32 gb
Best,
Brunno M Campos University of Campinas
Em qui., 20 de fev. de 2025 às 08:47, fsbuild fsbuild@contbay.com escreveu:
External Email - Use CautionPlease list:
version of freersurfer you are running OS name and version you are running amount of RAM on your machine
- R.
On Feb 20, 2025, at 05:58, Brunno M. de Campos brunno@unicamp.br wrote:
External Email - Use CautionDear all,
I run my script for longitudinal processing based on: individual processing (recon-all -i) + base image creation (recon-all -base) and longitudinal processing (recon-all -long).
In some cases (not always), the process terminates with errors, apparently at the same stage. The log states, among other things, "Reading texture...*** buffer overflow detected ***: terminated Command terminated by signal 6".
1 - I assume that I have exceeded my memory capacity. Am I correct? I have, in fact, written a script that parallelizes these processes, but I might be distributing the workload poorly if that is the case.
2 - If this is indeed the issue, do you know the peak memory required for such a process?
Thank you! Brunno M Campos University of Campinas
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1IUzS2y6h4Y-uKi9_ClfEXvfI-BZqyjZYW1FH8yQ7aalrdT... 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/16mCaEYEloV_DM7IXEor5EUDM-F-Yrc149dgB8zz8YtBeuD... < https://secure-web.cisco.com/16mCaEYEloV_DM7IXEor5EUDM-F-Yrc149dgB8zz8YtBeuD... . 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.
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Hi, I would also like to include here the entire set of lines I am using. Since there are three different parallel-associated flags for recon-all, I am also concerned about my choice (OpenMP).
recon-all -i Sub_1_Time_1.nii -subjid Sub_1_Time_1 -qcache -sd
./OUTPUT_DIR -all -openmp 8
recon-all -i Sub_1_Time_2.nii -subjid Sub_1_Time_2 -qcache -sd
./OUTPUT_DIR -all -openmp 8
recon-all -base ./OUTPUT_DIR/Sub_1_base -tp ./OUTPUT_DIR/Sub_1_Time_1
-tp ./OUTPUT_DIR/Sub_1_Time_2 -sd "./OUTPUT_DIR -all -openmp 8
recon-all -long ./OUTPUT_DIR/Sub_1_Time_1 ./OUTPUT_DIR/Sub_1_base -sd
./OUTPUT_DIR -all -openmp 8
recon-all -long ./OUTPUT_DIR/Sub_1_Time_2 ./OUTPUT_DIR/Sub_1_base -sd
./OUTPUT_DIR -all -openmp 8
Thank you very much!
Brunno M Campos University of Campinas
Em qui., 20 de fev. de 2025 às 08:50, Brunno M. de Campos brunno@unicamp.br escreveu:
Hi, thanks.
version of freersurfer you are running: 7.4.1 OS name and version you are running: Ubuntu 22 amount of RAM on your machine: 32 gb
Best,
Brunno M Campos University of Campinas
Em qui., 20 de fev. de 2025 às 08:47, fsbuild fsbuild@contbay.com escreveu:
External Email - Use CautionPlease list:
version of freersurfer you are running OS name and version you are running amount of RAM on your machine
- R.
On Feb 20, 2025, at 05:58, Brunno M. de Campos brunno@unicamp.br wrote:
External Email - Use CautionDear all,
I run my script for longitudinal processing based on: individual processing (recon-all -i) + base image creation (recon-all -base) and longitudinal processing (recon-all -long).
In some cases (not always), the process terminates with errors, apparently at the same stage. The log states, among other things, "Reading texture...*** buffer overflow detected ***: terminated Command terminated by signal 6".
1 - I assume that I have exceeded my memory capacity. Am I correct? I have, in fact, written a script that parallelizes these processes, but I might be distributing the workload poorly if that is the case.
2 - If this is indeed the issue, do you know the peak memory required for such a process?
Thank you! Brunno M Campos University of Campinas
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1sjikz6yK0UpP7uwVL4Jmd0-iE28t-gDUPiP3Ui7ckoAZ7e... 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/18JMl63Kxmq9xuM99I4ckAKJboJlk8cY6qRlZuhZKieNHrC... < https://secure-web.cisco.com/18JMl63Kxmq9xuM99I4ckAKJboJlk8cY6qRlZuhZKieNHrC... . 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.
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Brunno M. de Campos -
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