Hi Tracy,
I looked at your recon-all.log.
There are total of 19 runs. The first 4 runs from 2015 and 2016 finished without errors. They were all run on hippocampus.umd.edu. The later failed ones with segmentation fault were run a different machine - seahorse.umd.edu. Since you are using Freesurfer 5.1 built for centos4, I’m wondering if there are some compatibility issues.
Can you try running it on hippocampus.umd.edu?
I did notice that you tried 6.0.0 and 7.1.1 but those runs reported a different error.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Tracy Riggins Sent: Thursday, March 9, 2023 6:26 PM To: freesurfer@nmr.mgh.harvard.edu; Allard, Tamara Lynn tallard@terpmail.it-prod-webhosting.aws.umd.edu Subject: [Freesurfer] Fwd: Segmentation fault (core dumped)
External Email - Use Caution Yujing Any insight on this? Thanks, Tracy ---------- Forwarded message --------- From: Tracy Riggins <riggins@umd.edumailto:riggins@umd.edu> Date: Mon, Mar 6, 2023, 10:44 PM Subject: Re: Segmentation fault (core dumped) To: <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Yujing Yes, we have run this successfully with other participants (although it was a while ago). Attached is the recon-all.log thanks for your help! Tracy
On Sun, Mar 5, 2023 at 1:21 PM Tracy Riggins <riggins@umd.edumailto:riggins@umd.edu> wrote: Greetings FS experts:
We are trying to run recon-all -s -qcache on a handful of brains processed in freesurfer v5.1.0. (it's an old dataset...5.1 makes the most sense for our purpose.)
The error is below:
[cid:image001.png@01D952C1.6B05D390]
-------------------------------------- #@# 1/1 HMN080 Fri Mar 3 12:14:44 EST 2023 -------------- ----------------------- mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.51930/HMN080.1.mgh --sval /export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux seahorse.umd.eduhttp://secure-web.cisco.com/1241La8UANSF3aFvnvgmz2aBZoq4NP_I-Xg2zP9nsXxcY4aONgoneZ5-sAXRFXwbt-ifz1SW2xFxyQkOfaqEnD-XV7M2XwnlfIzVp0MhUkSnB2AQRIoZXQ4KJ-jWL_c-_iWGGNDOchXYLDrVxNx3Hqe91pj9dTuBogQhAQopasVfYqjA_Q4oObo1Q8CZEgd-NFs6FbUbgoCRsx6nBY9B_Y-Z674xtNPMoAm83W1IbtnTEbGHj1mt_2YRFnwmLPGfmmyOFDjm8iFw2cayKrkI_wO5sMnHDvBW0r3844_4kJaSMm92Lgp61N3oH9ogfOdSE/http%3A%2F%2Fseahorse.umd.edu 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8 18:13:21 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s HMN080 exited with ERRORS at Fri Mar 3 12:14:48 EST 2023
Can you assist? OR perhaps tell us where to find the core dump file, which may have more information?
-- Tracy Riggins, Ph.D. Pronounshttps://secure-web.cisco.com/15wAiYp1A8Jpo8jBJZdshwdMzWaNyB4fxtd5_lhEG04EuWCWsUMrHcr0ouzCJ9NN_jHOiVKV23omSiR_8ZPREj0EKe1GuhZN-vdOPoIbE3INrW3cSDpVCklwRRSHL37D_2fDnf7m_8PUzVat9HBLTR27uHEvqpFZ550I-jwVu7CINJEWISD516Eahdcrq4ufh3dRPzD-xmGzWwyLWAM8p8XiodRzyjrC2DxErje1nQvl7zLHpNvDaHLUE1IlZtX25XMzsNZDa-yaq9rsJP5a1OtnlkuZqkE3A7ROR0-dqsqXmiQwORluEG2oHjEX_Ydag/https%3A%2F%2Fwww.mypronouns.org%2F: she/her/hers Associate Professor of Psychology 4094 Campus Drive, Biology/Psychology Building 2147J University of Maryland, College Park, MD 20742 Zoom Meeting ID: 6751666548https://secure-web.cisco.com/1nA801X9aPl34ExfhmIqsB8n7JAuhOs7P8RPlnbm6yVwEYH-i4oHqla7YtOqLgaAy_3vuL8zeG68aClILxvNE6l6We60ihVyRUreALH85NmamMOOwLlvcLcKV0388XfXr27c-BcXR9vFcu7h3uZ-Uuz-oEGWvBrIdKl1zM6-enE3-YCSIDK8AfdAzOAGVvLv_4PG3fv74ByDbDxaGxWk-oQeAs4j2kDJhZhypRHe8OtfRLm58_2iuPd493XekBs2pKOu6bktOn_FV1Em5a6RLACzZ7ZWrN2Bb247W41dJR3sp5HtdJHyHHtssj0tlUFlY/https%3A%2F%2Fumd.zoom.us%2Fj%2F6751666548 ***************************************************** Research info: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://ncdl.umd.eduhttp://secure-web.cisco.com/1OXZSKXV26nbLZxbbXNJOYZ9E0NifXMMN8ZtEqQg7ZusmSd4C57VfgVQ6h-1bx7AiGUw7rl0FgzRDDt822JJ1K9_YW5khaB0VgytuGm-20mK0INNWTz9VWeS7jItXxMR2ClPBoEZ5lMtXbN9mCc2a3jHlfzIomK3AcHDPoLnEoelJH19jpFZGQEOpgsO0x-CUSkgjsezSGDhtjbz4mYuDCkgMjvSCe983UWCMMqjpxAuHi11gY_xGC5oIGb5PT-MYsPI7g0CkvEAUBMiDy7hd1Cpr3T3vJhe8oS3mcFb1O9-lvWOYLeQgXd-uTGFpYB5k/http%3A%2F%2Fncdl.umd.edu and MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.facebook.com/NCDLumdhttps://secure-web.cisco.com/1RElR-oGmLBKk11mKGpbdVhFTPRV5OJO3NlW5cRrF-0AsxVeVKjwFsuoXhRSszGgDmoqnnqTHzwSjl2NsonYit8h3YlpRsP0MWYNRbWQepkuHfL_CEsvMPYgH4UdyB0sNTJXWKCTTzKiM3LuxQBwWP0smiLXJI7wNMZOr1LlaO11ULTWGEeqn0IA5plvkF1OpFGwhVhfe2gAI_au8hQxkTi2HpB52BtCQlnuesecCm2-HzjpWm1n1oF0cuWWcwtMRxAt7uoNemT7MwOvDHK6cPstPEoVGZ80A3h2vcRu9MHpynAQLrPMq9Zm46x71faCk/https%3A%2F%2Fwww.facebook.com%2FNCDLumd Black lives matter in academiahttps://secure-web.cisco.com/1YlrNk6v-bahHVhsFijSj8glfi1Lwz2W71dAfzAgC0wpWQUKRDURQFiZ1nOU_Ef2eGdXdDwgebktIha6gp-DbAysTsdYESt_su5n6hVjcyFetoqDA6tLUi4DYXRnakgRkpY9IqsuEltMru-BL4mT0Q-mUbhhU1n7vDg-Y2HAza8Z3N4pAdfMqB8WHPG5yOFalyLopdFDw7bYY0TVODycptaOlsAyjSUbhQlNndcbMwqJaOe0hP6MiQG8yirDeZwpfPWHm6JJuYNXVbOfIHtWZ9RSsNOxCrXlkW5mnsVKKpFwiKHu_KU13pGMKO2QKKmA3/https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.1111%2Fgwao.12555 LGBTQIA+ Allyhttps://secure-web.cisco.com/1ZNpgjmML2m2L339a4oNfeN5d_bffblUDFCfEfFZmzJ-Rf1dCavhXtziwTFtrtNqcD4VtJUDb3TUqT9da4hD33tHL2TONJxNRrt3e5RT70ZYoD3vrqilQqFf4ILzukovzL2b9beyTEDnJAsnwi2yS8qKPOF0LmTpTfLmuyoC7cjz-TQ8tgKaywJdmjzs1dRz4AOGIU8gTyaWEU9S_SIPnolECsJZq8nf9FJpdGHpoF9VIhNApn66EJMQCqd7oMmb1qEyWeXxoW-UQ0V6EYyjE4Dh5ZZtyBA5IT_ivOaiqjmcX4_z2-Dxe9wABR9gUb0-c/https%3A%2F%2Fwww.accreditedschoolsonline.org%2Feducation-teaching-degree%2Flgbtq-youth%2F [https://secure-web.cisco.com/1zOCdkTzJs5sD68qwkpoy7zrkpSQSTIJVSYB7M7mYLemMlY...]
