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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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.edu<http://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.
Pronouns<https://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:
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