External Email - Use Caution
OK, I've attached the log file.
------- Original Message -------
On Friday, September 15th, 2023 at 2:59 PM, fsbuild <fsbu...@contbay.com> wrote:
> External Email - Use Caution
>
> It might help if you could send along the crash report as an attachment..
>
> -R.
>
>> On Sep 15, 2023, at 14:36, KennethSPrice <kennethspr...@protonmail.com>
>> wrote:
>>
>> External Email - Use Caution
>>
>> Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan
>> and got the "mri_convert: segmentation fault (core dumped)" error again. Any
>> clarity on this issue would be appreciated.
>>
>> Thanks,
>> K
>> ------- Original Message -------
>> On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice
>> <kennethspr...@protonmail.com> wrote:
>>
>>> Howdy yall,
>>>
>>> I ran a subject through synthsr (freesurfer 7.4) and am trying to run the
>>> output through the freesurfer 5.1 pipeline (the rest of my dataset was
>>> processed with 5.1). I am getting the error "Segmentation fault (core
>>> dumped)" during the mri_convert step. Any suggestions?
>>>
>>> Thanks,
>>> Ken
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/1n7fWOKSqI2VgPx35GDySYUjhvmIyBhf7FZreHbZZJS85Js0ir9bAdH9TSGhzmF25NdqiznSd27ygKVfTXb4XAHOXsyK5RWtBQkPNrOookPK6vLnvjbB1ShzSpqasaDrPBMaSFZBzb6XWC-L7JVJ1XFLi5491qO1VTcoYiT7Clp2PG4B2Sx_lLu_Um31g-Zu3mAGBgzo9C2ihGhL2ZsmOxYpylA_V34KCgCqbjtpzNRChwdDiGodk71jHdw_4_BfgjcaPHiVxhOO27vyg59nCvgT0BsXa6VuGip75gImbttHrWyMXEFm0CnDBFDab9Ilnei5iqjQ78C5E_F3MkeZD-g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Sat Sep 16 09:44:02 EDT 2023
/mnt/c/users/mri/desktop/2015/2020
/usr/local/freesurfer/bin/recon-all
-all -i 2020gre.nii -s 2020
subjid 2020
setenv SUBJECTS_DIR /mnt/c/users/mri/desktop/2015
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 PST
2023 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 7823
maxlocks unlimited
maxsignal 7823
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16643620 4367216 12047052 17720 229352 12142672
Swap: 29192228 0 29192228
########################################
program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:03-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:04-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:04-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:05-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:05-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:06-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User:
ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:06-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User:
ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:07-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:07-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp
$ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:08-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:08-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:09-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:09-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User:
ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:09-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User:
ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:10-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp
$ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:10-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:11-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:11-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User:
ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:11-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:12-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp
$ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:12-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User:
ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:13-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:13-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:14-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:14-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:15-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks
Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:15-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:15-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2023/09/16-13:44:16-GMT
BuildTimeStamp: May 26 2011 08:56:44 CVS: $Id: mris_anatomical_stats.c,v 1.72
2011/03/02 00:04:26 nicks Exp $ User: ken Machine: DESKTOP-MRI Platform:
Linux PlatformVersion: 4.4.0-19041-Microsoft CompilerName: GCC
CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:16-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User:
ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:17-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30
nicks Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:17-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:18-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49
nicks Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2023/09/16-13:44:18-GMT BuildTimeStamp: May 26
2011 08:56:44 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24
nicks Exp $ User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:19-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ken
Machine: DESKTOP-MRI Platform: Linux PlatformVersion: 4.4.0-19041-Microsoft
CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:19-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ken
Machine: DESKTOP-MRI Platform: Linux PlatformVersion: 4.4.0-19041-Microsoft
CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2023/09/16-13:44:19-GMT
BuildTimeStamp: May 26 2011 08:56:44 CVS: $Id: mri_fuse_segmentations.c,v 1.8
2011/03/02 00:04:15 nicks Exp $ User: ken Machine: DESKTOP-MRI Platform:
Linux PlatformVersion: 4.4.0-19041-Microsoft CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2023/09/16-13:44:20-GMT BuildTimeStamp: May 26 2011
08:56:44 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
User: ken Machine: DESKTOP-MRI Platform: Linux PlatformVersion:
4.4.0-19041-Microsoft CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/mnt/c/users/mri/desktop/2015/2020
mri_convert /mnt/c/users/mri/desktop/2015/2020gre.nii
/mnt/c/users/mri/desktop/2015/2020/mri/orig/001.mgz
mri_convert /mnt/c/users/mri/desktop/2015/2020gre.nii
/mnt/c/users/mri/desktop/2015/2020/mri/orig/001.mgz
Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 PST
2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2020 exited with ERRORS at Sat Sep 16 09:44:21 EDT 2023
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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