External Email - Use Caution
Hello Freesurfer Developers
I am trying to create an average subject for 20 subjects using the function
make_average_subject. But I keep running into a segmentation fault. I have
attached the recon-all.log file.
I found a few other posts about the same problem which direct the users to the
following patch:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/)
But this patch does not have a readme file which can instruct the users about
the steps that need to be followed to get rid of this bug. However, I have
replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME)
with the files given in this patch directory. But the problem still persists.
Kindly provide the steps that need to be followed to make use of this patch
properly.
Regards
Himanshu
Sun Sep 15 16:15:08 IST 2019
/home/leesa/Desktop/freesurfer_outputs/avgsubject
/home/leesa/freesurfer/bin/recon-all
-s avgsubject -cortribbon -aparc2aseg
subjid avgsubject
setenv SUBJECTS_DIR /home/leesa/Desktop/freesurfer_outputs
FREESURFER_HOME /home/leesa/freesurfer
Actual FREESURFER_HOME /home/leesa/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux sinha-Lenovo-Product 4.15.0-62-generic #69-Ubuntu SMP Wed Sep 4 20:55:53
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 16384 kbytes
maxproc 96050
maxlocks unlimited
maxsignal96050
maxmessage 819200
maxnice 0
maxrtprio0
maxrttimeunlimited
totalusedfree shared buff/cache available
Mem: 24633364 321609613523204 84196 789406420933832
Swap: 18431996 018431996
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2019/09/15-10:45:08-GMT BuildTimeStamp: Jan 18
2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp
$ User: leesa Machine: sinha-Lenovo-Product Platform: Linux
PlatformVersion: 4.15.0-62-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2019/09/15-10:45:09-GMT BuildTimeStamp: Jan 18
2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve
Exp $ User: leesa Machine: sinha-Lenovo-Product Platform: Linux
PlatformVersion: 4.15.0-62-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2019/09/15-10:45:09-GMT BuildTimeStamp: Jan 18
2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $
User: leesa Machine: sinha-Lenovo-Product Platform: Linux PlatformVersion:
4.15.0-62-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/09/15-10:45:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58
CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User:
leesa Machine: sinha-Lenovo-Product Platform: Linux PlatformVersion:
4.15.0-62-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2019/09/15-10:45:09-GMT BuildTimeStamp: Jan 18 2017
16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp
$ User: leesa Machine: sinha-Lenovo-Product Platform: Linux
PlatformVersion: 4.15.0-62-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2019/09/15-10:45:09-GMT BuildTimeStamp: Jan 18 2017
16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User:
leesa Machine: sinha-Lenovo-Product Platform: Linux PlatformVersion:
4.15.0-62-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/09/15-10:45:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58
CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User:
leesa Machine: sinha-Lenovo-Product
