External Email - Use Caution 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 <bru...@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 <fsbu...@contbay.com> > escreveu: > >> External Email - Use Caution >> >> >> 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 <bru...@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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1sjikz6yK0UpP7uwVL4Jmd0-iE28t-gDUPiP3Ui7ckoAZ7evEKKVoaELXUeoJYNxh6LPVM9cK-x3imtf9ylilr21PWMnYwpuNUFrAeqJYRU1E9bqJzscCswXO6sly7-HLAfXdnysWuLhsihdVVqkLpJ8tpS8vdRCy0fWe3I2G5zi6PAxkWsyq5v_jr6an09nLgmZgFe9OvlAnBuDOWWeawp3_Tdxt-0FcRf8Nd0cW3kafm4tN4D1oH-rzPxDQrO9td01hGsBuB3rtVD9lAeWkKDgTQQpZ66uke1j3PaMQHJSNSSmea3mwZSQCvYOcRbvSab3aniYpzHkJxoS_j0zc1g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1sjikz6yK0UpP7uwVL4Jmd0-iE28t-gDUPiP3Ui7ckoAZ7evEKKVoaELXUeoJYNxh6LPVM9cK-x3imtf9ylilr21PWMnYwpuNUFrAeqJYRU1E9bqJzscCswXO6sly7-HLAfXdnysWuLhsihdVVqkLpJ8tpS8vdRCy0fWe3I2G5zi6PAxkWsyq5v_jr6an09nLgmZgFe9OvlAnBuDOWWeawp3_Tdxt-0FcRf8Nd0cW3kafm4tN4D1oH-rzPxDQrO9td01hGsBuB3rtVD9lAeWkKDgTQQpZ66uke1j3PaMQHJSNSSmea3mwZSQCvYOcRbvSab3aniYpzHkJxoS_j0zc1g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> 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_JmBbeGRrRMHYhFu6zP6fXhP_ba2mNogEl8OW5w5uowsXOevnazzh6fg2o5spOZXv-ryempz7oHFhQFkvvYDtjoPt_fLEm-a8xqTXQlJqHgSSaDUqHCfjieK1G3HG87hq7j6KmE5XSFZ-JnK1Dda8pZvRIspJfp62XztKA5DBFxyh5u0mWK2WcEVhvw-HO8uXn2cR16LCUOVPKj2oVVLbfgdTjFq7UVhzRvWGBaOi0zQJGVFZBK_EHmeAjyG3zpPMtt5OoBwRcdM1tKB-HJt6vc5OFHP9jAIe2e-Stsg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> < >> https://secure-web.cisco.com/18JMl63Kxmq9xuM99I4ckAKJboJlk8cY6qRlZuhZKieNHrC_JmBbeGRrRMHYhFu6zP6fXhP_ba2mNogEl8OW5w5uowsXOevnazzh6fg2o5spOZXv-ryempz7oHFhQFkvvYDtjoPt_fLEm-a8xqTXQlJqHgSSaDUqHCfjieK1G3HG87hq7j6KmE5XSFZ-JnK1Dda8pZvRIspJfp62XztKA5DBFxyh5u0mWK2WcEVhvw-HO8uXn2cR16LCUOVPKj2oVVLbfgdTjFq7UVhzRvWGBaOi0zQJGVFZBK_EHmeAjyG3zpPMtt5OoBwRcdM1tKB-HJt6vc5OFHP9jAIe2e-Stsg/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. >> >
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