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Hello FreeSurfer Developers,
I'm want to run HCP T1W data of recon-all , but it always failed on step
" WhitePreAparc lh", below is my run information:
OS: Ubuntu 22.04.2 LTS
MEM: 32G
CPU: 16
Freesurfer Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Command:
export SUBJECTS_DIR=$(pwd)
nohup recon-all -s $1 -i $(ls *${1}*) -all -qcache -3T -parallel -openmp 16
-threads 200 > nohup_${1}.log 2> nohup_${1}.log &
Error messages as below:
mris_autodet_gwstats done
@#@FSTIME 2024:02:06:05:28:14 mris_autodet_gwstats N 8 e 5.75 S 1.02 U
8.70 P 169% M 277604 F 3 R 131626 W 0 c 403 w 6466 I 0 O 8 L 1.96 14.01
13.54
@#@FSLOADPOST 2024:02:06:05:28:20 mris_autodet_gwstats N 8 1.96 13.81 13.47
#--------------------------------------------
#@# WhitePreAparc lh 2024年 02月 06日 星期二 05:28:20 CST
cd /home/tben/ds000102/HCA6139970_V1_MR/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
--threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
7.4.1
7.4.1
cd /home/tben/ds000102/HCA6139970_V1_MR/mri
setenv SUBJECTS_DIR /home/tben/ds000102
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
--threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
Command terminated by signal 11
@#@FSTIME 2024:02:06:05:28:20 mris_place_surface N 18 e 24.22 S 4.47 U
1.71 P 25% M 185596 F 9 R 46047 W 0 c 184 w 12734 I 1296 O 0 L 1.96 13.81
13.47
@#@FSLOADPOST 2024:02:06:05:28:44 mris_place_surface N 18 69.96 28.86 18.46
Linux tben-dev-server 6.5.0-15-generic #15~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Fri Jan 12 18:54:30 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s HCA6139970_V1_MR exited with ERRORS at 2024年 02月 06日 星期二
05:28:45 CST
For more details, see the log file
/home/tben/ds000102/HCA6139970_V1_MR/scripts/recon-all.log
To report a problem, see
http://secure-web.cisco.com/1gYb-2hE-QjkoVlTlGmx1IVV7-IUAB7paWJo1QUb0Vj4ezaR8LII1FERoMOISc_G5vLoz5lviLvaCMZaELkJ2MygS0ul9Dn3JBIV1RtRd1vO54v1TRxAu-YgSDRTI8jIR5W27dmKjmog1Kek_A2-1Id2MidRaj88bWYvsm5ySBraq1DqvrdRXiG6yRjd-L0lIxzODdeWhPhlWqqCqndfjUT9Mm83VdOTTiDipArhYBg_JDQOFt-a5vfYqkg8TKn9EKe15CHXj-qtEEhOAM07Skpg607mhQ025411Y-LcyB7XJRl8KoQ09R1Ii0aUZ88PVvmqTx3p-JAPVS-SuSu8npQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
Check the core dump file under /var/crash
vim _opt_freesurfer_bin_mris_place_surface.1000.crash
ProcStatus:
Name: mris_place_surf
Umask: 0002
State: S (sleeping)
Tgid: 23410
Ngid: 0
Pid: 23410
PPid: 22657
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 64
Groups: 4 24 27 30 46 122 134 135 1000
NStgid: 23410
NSpid: 23410
NSpgid: 23410
NSsid: 22657
Kthread: 0
VmPeak: 10878292 kB
VmSize: 10394436 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 185500 kB
VmRSS: 185500 kB
RssAnon: 179356 kB
RssFile: 6144 kB
RssShmem: 0 kB
VmData: 2068316 kB
VmStk: 132 kB
VmExe: 3084 kB
VmLib: 3820 kB
VmPTE: 1772 kB
VmSwap: 0 kB
HugetlbPages: 0 kB
CoreDumping: 1
THP_enabled: 1
untag_mask: 0xffffffffffffffff
Threads: 200 SigQ: 0/128234
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000100000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 000001ffffffffff
CapAmb: 0000000000000000
NoNewPrivs: 0
Seccomp: 0
Seccomp_filters: 0
Speculation_Store_Bypass: thread vulnerable
SpeculationIndirectBranch: conditional enabled
Cpus_allowed: ffff
Cpus_allowed_list: 0-15
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
Mems_allowed_list: 0-1
voluntary_ctxt_switches: 21
nonvoluntary_ctxt_switches: 17
Signal: 11
Uname: Linux 6.5.0-15-generic x86_64
UserGroups: adm cdrom dip lpadmin lxd plugdev sambashare sudo
CoreDump: base64
I use 3 different VMs to run the same sample with different freesurfer
versions , 2 are 7.4.1 and another one is 7.2 , but always failed on this
step , I don't know what's the reason cause this failed , can you please
help to have a look ? Thanks a lot .
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