External Email - Use Caution
An applications process(es) can be killed by the OS when the application requests more resources then the machine has to allocate, e.g., it requests too much memory, CPU resources, etc. So it could be your Linux machine does not meet the system requirements to run 8.0.0 as listed on the download page, https://secure-web.cisco.com/1XfLimZ9aSU_VUKvX9FsGRHZ_qGVoPimFd5L19Q1cvSCoFFrfCTWX-RR7Qq59bhM9m0-CQBTPHdVeUCzxncmdrU0nI_CApkewVOuHEYOnFPr37BKCXLu2LvB5pZhiBTmNd_cDTgxo0uR1ZV2yedt_B8Gvh4VKfEiILe23ObXqIXz0lX9vIF3ts107BhWvm3o54kvNgLbeZr_7ianbRmV07UX0HLr4GQ7zYiwrEn-aYLidPLsnCexBfjTJ0L8CvzLZmOQkyiVbyhlw42-NiF4wfFHOU4YWGbchUcnisRZOjE5DlsYM1PUNH96MF92UTRSjBq0-EYqDZ_6fP3qrkIfJdw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads If the total memory on your Linux machine is not greater than 16-24G, and if you don't have more then 2 CPU cores, then the Linux OS plus some Freesurfer commands like mri_segment_hypothalamic_subunits (that make use of tensroflow, keras) might not be able to run. - R. On 3/10/25 07:57, Payam Sadeghi Shabestari (payam.sadeghishabest...@uzh.ch) wrote: External Email - Use Caution Hi FS dev team, I tried to run mri_segment_hypothalamic_subunits with my ubuntu 20.04.6 and FS 8.0.0, and MCRv97. I tried both using cpu and gpu, but it returns me the “killed” message when I use 1 thread and another error when I use multiple threads. Could you please help me with that? Best, Payam ubuntu@sch-mri:~/data/subjects_fs_dir/nalq/mri$ mri_segment_hypothalamic_subunits --s dvob --sd $SUBJECTS_DIR --threads 1 using 1 thread predicting 1/1 Killed ubuntu@sch-mri:~/data/subjects_fs_dir/nalq/mri$ mri_segment_hypothalamic_subunits --s dvob --sd $SUBJECTS_DIR --threads 2 using 2 threads predicting 1/1 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/10EQ9krC53_12XYzxHC6HdHgIEt7f-cQEe-AETPMBBGn3K5YIZaneGsBtvLOE34R9zBdq0ghj9P8txTB6RrTouKZjIKF5ABozkx1bcc4W4LlodXWhz5iLoLPNd1bVTHlS0kkHzdz5iC1wojUkmYjBiGJNsO1DtLLepfRnK358Bv-fY10tiwxOeJeabo-Nx2W1T1e_rAlLlZ-u-1hq0STz86_JX42_E5QK_RgVrrqZDiBfsYYmM2WyeBRf12UntbhxIa4u-L5loz6NS4WKNbXwHHcaXnV1trg93kc9cHm7a1WZqW205nwN-OuZIDajhPQLEX2yOhSKtLgX6OS9ogIsDQ/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/1ezXR_c9HnboqD4n7PzBYWLoG4tcP9ioNq3L6SV9rjkMyHUhWGvYr1L3ZysKQVTBNgSW0XvIk7rHqlSvBJy1C8Y68q4uZjNmCv_7wHjsq-S23UCA_u9sMnO2pi8TfkoBe3h0EiLyraKQtEiLdS0Cno2lXxQn_BUPhqtWxPNXTv1HDOxMnqiA6yeQB0r7HibG3FQL9Zki1Y2jrG1jPU24gFaiqm090S9Am6UBAboDQyr2zi9neYyzi6Zp8tGrEjG0u-ySKKSXHv3bNkff8OrAqUlZbB01oDoKuYRtyXPX5VKI-SMFFcuzLIaCPI2KKFJMiluduRvuo4yYtldxJfZ9yyQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1b7ppWt6UMZVc6U9riBaenK-Ml1AGuj4ZcuZ3jwJT7BXIO-dnQyZyHo1mBONq8MmbKQZbHxkP5r0C7LjfQCtpfK_RlQACz5kv4EOhgxJAY5KQD9PMwylV-Dy5FuKn5lYdeox5kFqYau6DUtyifIhqa1L-FCuLv8urrA9ph605ql4g-tcZen2SGm8NhEklfI7Bk03HaRkSPJe9-YqFxU--bdo-ALGcu7wf7YWxN5DFNthc780ZtGdb5K6noVSEzY38hwqil59znN1k8lnGxz9o6aQjoMeeJL2hK3Zfx-yBlxe_zWhe7Zd49uEe65OU6YteKHi2LrTKaE30fmKhyv9y7Q/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
