External Email - Use Caution As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and binary backwards compatibility cannot be expected to work indefinitely going forwards to newer versions of the OS. I ran a simple mri_surf2surf command from 5.1.0 on CentOS7 and it crashed immediately. I then tried the same command using the freesurfer 5.3.0 release built for CentOS6 and it worked on CentOS7. You can download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz from https://secure-web.cisco.com/1S9OGgcf17zFMWWXjC8lPSf7mq4hk6Ou69iX5K_AOeoFHBHE1rQWdgSQHIJ_NltdQVPZxZqenztI4e0UJYoQYXV3RyG2hJ0p6RJY0ZIF1xiGNLjsAqHVtFzV-oYtD7aR31DLQHblFXxEfdBX4Vql5LsoS1jWskUTjd4ntP3gb7W8JljRuIJ6MdG4y2wQuI-GaUJuuT399EFLgqUr2C8OLSGDhSiKtR1RypfNisWBhewJ3AJwXj1EB7tLC40-LCheI9AQ32FDTRLpd_nP3Q7es7dX6x8pkMJ2VDObLXlcjvI-8ShfLmCvS2Qt5SAGlHO7eN0lERi-87Uvh9cB-88yPXg/https%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0, or see the direct link https://secure-web.cisco.com/1O5P1_jnLPrOGdYkXFNDEb2y-k3m7evHo5fe2uNzyoNAaKSkB3Nt1_wXhgDLemrYevJFPQsp5tpz_wdWUjWhVTD9p6CNaNieHzYFY7XvcOkTsvaaxQ14203xL-zEAR2Eav2sKtvuxzucTJqIFKJcJxwO4tU1LWxZbL8HSzpbAx4gHo4SUez6Lwz1bZarwjhy7YEdn5NslhRbXzeF8MIl4YiwsVYH1XGmK-teHPP1FTJiVcnLV6oEDyz9jwP0uUf5tP9RGIWsdKBnItP4JbrHc-fZumOroSi_i6GuKCOsp-IouIjFOvOowWaI6ldL4IOMcIeaqNW-BG-wO4CN5ByZFrg/https%3A%2F%2Fftp.nmr..mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz%26nbsp; The 5.3.0 release notes are here, https://secure-web.cisco.com/19Gm_LLMuws0ked03zCf5tnQ6jPznJWqxPjwPpXVopC8p78rjNPZ0vz5xHrO2aKd8JSQ_XBuTZpdyTiuLntQAt2liEN6ADvarGfFSsNQpi2aX7V381p7Ge6mf5WU5sRikpf1mKfnk7bhxPpaf989Wn2Ad5LHDhURmyUJsLmE10pPUbR0wmI4GxQmnYUgxfBKxW5KlTfGnRYqISbDzEt3AAgC4ySUX6Q1oVM8C5-9U76ewGqDghhnp63RAKID6xs8bIv9L6XPaRhuR5pd3xJGBnSbadKj8KnS2SQqtNx37UVmfb6uy3_ZAn2el2H1Us6bCfLHtVITooxrEC4eSAjcT3g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPreviousReleaseNotes Please be aware we post this caveat on our download page saying that numeric/floating point results can differ when you switch to a different freesurfer release or newer version of the OS, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). I would expect the above to be true if you switch from the 5.1.0 release to the 5.3.0 release. So if you must continue to run 5.1.0, then I would try to run it on the (same) version of the OS you used where it previously worked. One way to do that is with a virtual machine (VM) hosting the (old) OS. It looks like we have a virtual machine image with freesurfer 5.1.0 installed available from under https://secure-web.cisco.com/11VzvQh0Sbki3c91H_Wr1_Sbun-1WBJp0X7FROYdV5ww4P1XCrnuHgTtkzTQdl3_7AkU0UmLpg0fbJW_x6iz4-U-kOtcmTNunqDxApQ6jSiFtYVyLzfuwj_-yW54KE5w2FHUetO3j9bOHvxGmB4LkVaIqw_2rMxgO6mtkwj5oLy69L80AR5X8-Zym75Z39agFLdE3vsBF8kyyH6z97FHHYh6zl74H5dUXemQ13bgiLVqzmQ7c0Yx332U9cw4tF-G7t5mtQeJAXsr3_7PMVbI5ta6WKVv_zg_wZ2JFre6kFAExWj6KYkj8A1RTKXYv3JuY4cuFaKz621J4AGMEFALYHQ/https%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.1.0%26nbsp; That virtual disk image file (..vdi), https://secure-web.cisco.com/1f9gnsQF3U_bgE7wRs0_PPUaeSlPgrJxG-afglho7qOnEI6IK3x6Q74lVczCqUz814qnE3gT4GO-FHPsn6fv4NwsG7SMQykR-ghIZUMdjGSmckggj6M5NAUe9S37AMJzV215rTC59h7VmVa-paqybjKPfVK-VAtQ2oUwks-053E4KC89mt53wvYjRuyAhnLrA0JFdOGOuMo-8KrX_ENyyGH2zzQJtiTEGmBnnMpKIGFw9QCAfWRqmgMi_BDHy7lmAxYnWCVd_XdH1VJ1HqLhBIonwjm5X2caNf1OTebriIZfm2h5IupSjvLGZMRF43ej87-9ybXcYkIZ6L_qBDq_D-A/https%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.1.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi, should still run in virtual box on your CentOS7 machine. My guess would be it is a CentOS4 VM image with freesurfer 5.1.0 installed but I don’t know how that matches up to any previous version of the OS you used to successfully run freesurfer 5.1.0.
- R. On Mar 9, 2023, at 20:17, Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Tracy RigginsSent: Thursday, March 9, 2023 6:26 PMTo: freesurfer@nmr.mgh.harvard.edu; Allard, Tamara Lynn <tall...@terpmail.it-prod-webhosting.aws.umd.edu>Subject: [Freesurfer] Fwd: Segmentation fault (core dumped) External Email - Use Caution YujingAny insight on this?Thanks,Tracy---------- Forwarded message ---------From: Tracy Riggins <rigg...@umd.edu>Date: Mon, Mar 6, 2023, 10:44 PMSubject: Re: Segmentation fault (core dumped)To: <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.logthanks for your help!Tracy On Sun, Mar 5, 2023 at 1:21 PM Tracy Riggins <rigg...@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: <image001.png> --------------------------------------#@# 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-cortexSegmentation fault (core dumped)Linux seahorse.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/Linuxrecon-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.Pronouns: she/her/hersAssociate Professor of Psychology4094 Campus Drive, Biology/Psychology Building 2147JUniversity of Maryland, College Park, MD 20742Zoom Meeting ID: 6751666548*****************************************************Research info: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/16uU9Voo_CziLp-ng0Dkh27qT2SP4MKOfHHDUkDJsl9KxO269sXBuDOGn0L3BLS6BTC-MpXQfJqX8tC7c16K1cjvt9X-3gigckZUu3N9uMbKd5VvPeSr5gZ9IicJF276UJRMSoSQKVXfjtdAPfMi4OteaROYoPXDAFObh2aZwYYgvfIH-3fnh38lUMmXr1hbqJ8d5Q-O5XLQWkN9jCL8EirJgEGWFFVoEx1tk6uhFvxGTx2bQ6PUruggZrlow3XSQDkkgWZ3PQLuIpUPpSOeMt_xyLcau81G3CXiKel6heSXeyRcCKl7KnZVpHTTrl5zefsDUQpaIejwKrIOP82u5Dw/http%3A%2F%2Fncdl.umd.edu%26nbsp;andMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1OFC1dVVEqctiVCBhWLVpuWAqvx-VAFmj5QcsNYIOUdeX23sBRJGiYMW-2qrEBsUprvt8ic2wR_pyGVg8UyyahtNCirbXSy1admHRUJJ2lhb7Cwb5flXzy55YrOsfS-X6GQGH89SlW6IwIg7vUAQmK18R7YuRRRp8qoaiJQQuxTSGCLpogmMR43wA5815qxEzW94NSKvK5_x-A59DxwZSSAPbP8J8sKTlFnlCyywsinFxBF2oMWAEaCDOxaPZbnMLmqO91KHUeavhrzTmKWVcPiohSZr2ovA79XcUTGOeWuMyNV2IsTVVk0JELMM5iDAGnOlf73qwelV-3NvDpOzQUA/https%3A%2F%2Fwww.facebook.com%2FNCDLumd%26nbsp;Black lives matter in academiaLGBTQIA+ Ally _______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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