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 Riggins
Sent: Thursday, March 9, 2023 6:26 PM
To: 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
Yujing
Any insight on this?
Thanks,
Tracy
---------- Forwarded message ---------
From: Tracy Riggins <rigg...@umd.edu<mailto:rigg...@umd.edu>>
Date: Mon, Mar 6, 2023, 10:44 PM
Subject: Re: Segmentation fault (core dumped)
To: <freesurfer@nmr.mgh.harvard.edu<mailto: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
<rigg...@umd.edu<mailto: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:
[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.edu<http://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.
Pronouns<https://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
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