Hi Tracy,
I’m wondering if you have any success with other subjects. Can you attach the failed recon-all.log?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Tracy Riggins Sent: Sunday, March 5, 2023 1:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segmentation fault (core dumped)
External Email - Use Caution 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@01D95008.DF0111D0]
-------------------------------------- #@# 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/1bL2Kx55VdxPIM67Q171_sd70HWT8U-Mm8YVRuBJ1GK5bWDKzhfTdcdSCHEuzkJlybba1FR7lC96jONKs2DutOWvQvQpLhH7nZigZkQCD3TD12tsqYcZxoS3go3R9rxOA1A3wUrldoUq3VQ8FgLpBhMmMbxy4I-CoTkh4RFMRjKtBfq2YjLH-tGXLHZcw-fEVb7kzAkQf5mB_Nc-JzoZsxgTbFqbscufFbsNgkVkUXqjS0kJSM7biqnKZxisZC-7imCMT61EsjDB3dRuXQ3xBR-0hYql0-_9qu5ePjEk2KxEr67_as6rtR318ZYnTHzKtu6fqVCJIEz0QZfAwzlHfSg/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/1WTjrK6XJwG7-24mUYPAFcId6puqiKxHmofCChPCQb4mC-POspjoZDwtGSsSFXgAC4v2YKY3FCnjy58JL6_3vxhCUg0QkC27LhQ47hQqR-36j6tFyrseV_UkPSGnwS0OOVXiAa8tCUIYtzXJubvxHo746UTXO7k4bZllvRKTm_1XZJLNayue3qQvCDZ92lFc_xa_2WtR-P_qnPPpCXwFxyIRGcq1HwvAbcuEB7PsCmZvm6ZA7-mQkCv4VPAW2XW22aml_Fe4eSXDT0Jkw3xq-d5m_lN1z-2Ujq-gJNcYYF_XK8Gokq6YkVKSuw0BorhYT4kibFE30CsLAIj0kvXNyXQ/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/1hviwkViTW16JTEvWH-47gs1rSV1H4pi6BZD9e1QCPEJ2VUmxkRkg32zOyDlXxrU73I_4AlSQ_0Rg0WXkzu1wMeZJKHXwHVU0mKmeJpy10wdHObQoFD2_FU5dPOVdPlD-5CPmKqtT6JgYOKya9RbQuNqEkz4KRKHZlgwYu9JVG-D7i1njuR_AkzfyRUTmy0nm9AxWU-HgQHO4AbcOjmW8WpdrOCHAxvflzuikmineX4_L5cS6bzDwYVW5UHm9UMb-br_PK89fz5ItVXECLYbh3N74g2tb0-9CJ1XVsQhTpMvxlPjCk1kK7WiO0_hzJqQ__qvWg9fhm9CeqodrZGLQPw/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/1JWrYfqglbLMQuNvUkCI3__mdHJZE-j2I4GZAMwxbYavfuRQfdHTN8Fb8O-hN07nqDsGoHPJbXTMhVpJJQcb_CkXCFgW_Spl6deT8olpw0za5mcWw_IMIBc4ip0tJ-V316-47g1p79Y9ifrfUwiU00KKudbClq_eezPmENt9UeEUmKIafocXLCRHHAjpqvBF87TaCJmkKB55WvpT25kbIZOd_ztdYNYcvAqF9Ynpd0GVjJZBH0MkVdbTiwzOXxXOEGXGUPI6OIU8fyNW3MkA0Czgf4W8BWQ-jrI8lRBCii8iNhOlgQf2kR1KAMjM5VWKgyK6NYVLmdGQ-2n9vUBdZ3A/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/1gMMoT_3zpTn_EJwufCskhV5rA9d3a3dfl-3blyeCnoRvfBV7IOLXCKFjnjtNgy9plsB4KPUM6PJnffPRwzHhudjzlZdUtkSr6tT8Ll8K0IqNRTnxxw1FHkZWYdn2X8MeEIJE8m0IRGMGz9QNeHoRGBLZPWXfpxB1BANB37541RqCqISXkibM62PuhEvmbwxgowSX5h3XquBQeQz56_aWDBc0JZlygwU9AzLlI_K90JGuRb6pOPtxVH8phbxilsQjf-emecx5wT5EScisBR9FYg7i71C-1pp03fSZVxcpulQpJEGECtYqg9p7nab0sNPMuZoUrCfBHjZdl58NRn9qtw/https%3A%2F%2Fwww.facebook.com%2FNCDLumd Black lives matter in academiahttps://secure-web.cisco.com/1J1h-u95rDMtqm8NNRIKxQgXcKxqK0HepLClZ-LZRNQ_s5O43E5sztWTAPOxeZ7h4zx5Ri_mAHBrU5JIsZjf9ERyRiqWmJ7EAtRJu-Rcs-E6SeSXs-f4VyK8uvv8wHQnl-7xct0QenGwETa7zLHJ4cKqSx3aj6zrB2rL_4yqZZPKQSDKegM61sR9ARGEq6zeTjvBGXasbo8bQUXkZE5tMAkui9ual5FCK4qnN_x3UNarLnxWeWGZjlaQUQiMsL8_RC21FzzrStt7jlJieV-yZLBWn1FerkEisKQtKLa2T-3lurw_AKTXIXvr-b3YXCnKItfpNJzi593heQ42ZhtsEkw/https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.1111%2Fgwao.12555 LGBTQIA+ Allyhttps://secure-web.cisco.com/1gzE6oBTSI-WE3shKwya1t2cvYue63e9MW9Tseqcx37BoslP7RFrWfwpNpRwp_FGI11HdxX5r4oOhXjt8OpMosy8OvWm5daKI58oMmVGi-GCq9TR_iJjdjWvpYnPnqVe6zY__S5HdP6oGk0ZE7uV_blHpaM0SY0r5OaNDCWB2UJdo5e5VQjHXWhs8zA5hdtxYnk1rCYS0Ju1o9RFOoBnfe5_uqBpQa5S_6uOg_uDEEwVUymz1ZdBQc9wBrc0HOvjA07jUKJMugbivK_x4wM_aP1gJ4C75Wb55h6Hk3nNiC_fD2NZ3nJLFwZB9e5JfmeiZzW9u2TMlxt8HOvuqZdq3Gw/https%3A%2F%2Fwww.accreditedschoolsonline.org%2Feducation-teaching-degree%2Flgbtq-youth%2F [Image removed by sender.]
