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.edu>
Date: Mon, Mar 6, 2023, 10:44 PM
Subject: 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.log

thanks for your help!

Tracy

 

On Sun, Mar 5, 2023 at 1:21 PM Tracy Riggins <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:

 

 

--------------------------------------
#@# 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 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: she/her/hers

Associate Professor of Psychology

4094 Campus Drive, Biology/Psychology Building 2147J

University of Maryland, College Park, MD 20742

Zoom Meeting ID: 6751666548

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