External Email - Use Caution
Thank you for your help !
I have run the command:
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and got the nucor.log.
-----原始邮件-----
发件人:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
发送时间:2021-06-01 08:35:38 (星期二)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)
Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and send the file nucor.log
On 5/28/2021 7:51 AM, liub wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes of
running,there was an error:
mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul
Segmentation fault (core dumped)
Command exited with non-zero status 1
Also when I ran the command "recon-all -all -s bert" using the official data in
*/freesurfer/subjects/bert ,it raised the same error. I googled this error,but
there's still no answer.I've attached the recon-all.log. The recon-all.log is
belong to bert and recon-all(1).log is belong to my data.
Here is my operating system info :
uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22
00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Platform: CentOS Linux release 8.3.2011
FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1
Thank you for your kind help.
Best regards.
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 9 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = nu.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --uchar
shift
switch ( $flag )
switch ( --uchar )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set talxfm = $argv[1] ; shift ;
set talxfm = transforms/talairach.xfm
shift
if ( ! -e $talxfm ) then
if ( ! -e transforms/talairach.xfm ) then
set DoUchar = 1 ;
set DoUchar = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )
set flag = $argv[1] ; shift ;
set flag = --n
shift
switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 2 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 2
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 1 != 0 )
set flag = $argv[1] ; shift ;
set flag = --ants-n4
shift
switch ( $flag )
switch ( --ants-n4 )
set DoAntsN4 = 1 ;
set DoAntsN4 = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
if ( $DoAntsN3 && $DoAntsN4 ) then
if ( 0 && 1 ) then
if ( $DoAntsN3 ) then
if ( 0 ) then
if ( $DoAntsN4 ) then
if ( 1 ) then
which AntsN4BiasFieldCorrectionFs > & /dev/null
which AntsN4BiasFieldCorrectionFs
if ( $status ) then
if ( 0 ) then
endif
endif
set cmd = ( which bc )
set cmd = ( which bc )
$cmd
which bc
/usr/local/ashs_Linux64_rev103_20140612/ext/Linux/bin/bc
if ( $status ) then
if ( 0 ) then
goto check_params_return ;
goto check_params_return
set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname nu.mgz
mkdir -p $OutDir ;
mkdir -p .
if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log
./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/home/liubing/FreeSurfer/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
--ants-n4
tee -a ./mri_nu_correct.mni.log
--debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
echo "nIters $nIters" | tee -a $LF
echo nIters 2
tee -a ./mri_nu_correct.mni.log
nIters 2
echo $VERSION | tee -a $LF
echo mri_nu_correct.mni 7.1.1
tee -a ./mri_nu_correct.mni.log
mri_nu_correct.mni 7.1.1
uname -a | tee -a $LF
uname -a
tee -a ./mri_nu_correct.mni.log
Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC
2020 x86_64 x86_64 x86_64 GNU/Linux
date | tee -a $LF
date
tee -a ./mri_nu_correct.mni.log
2021å¹´ 06æ 01æ¥ ææäº 21:45:07 CST
set templocation = $OutDir
set templocation = .
if ( -d /dev/shm ) then
if ( -d /dev/shm ) then
set shmsize = `df -m /dev/shm | tail -1| awk '{print $2}'`
set shmsize = `df -m /dev/shm | tail -1| awk '{print $2}'`
df -m /dev/shm
awk {print $2}
tail -1
if ( "$shmsize" > = 4000 ) then
if ( 64177 > = 4000 ) then
echo "Found /dev/shm , will use for temp dir" | tee -a $LF
echo Found /dev/shm , will use for temp dir
tee -a ./mri_nu_correct.mni.log
Found /dev/shm , will use for temp dir
set templocation = "/dev/shm"
set templocation = /dev/shm
endif
endif
endif
endif
if ( ! $#tmpdir ) set tmpdir = $templocation/tmp.mri_nu_correct.mni.$$
if ( ! 0 ) set tmpdir = /dev/shm/tmp.mri_nu_correct.mni.2576084
set tmpdir = /dev/shm/tmp.mri_nu_correct.mni.2576084
mkdir -p $tmpdir
mkdir -p /dev/shm/tmp.mri_nu_correct.mni.2576084
echo "tmpdir is $tmpdir" | tee -a $LF
echo tmpdir is /dev/shm/tmp.mri_nu_correct.mni.2576084
tee -a ./mri_nu_correct.mni.log
tmpdir is /dev/shm/tmp.mri_nu_correct.mni.2576084
set MaskVol0 = $MaskVol
set MaskVol0 =
if ( $#MaskVol ) then
if ( 0 ) then
if ( $DoAntsN3 || $DoAntsN4 ) then
if ( 0 || 1 ) then
set numnc = $tmpdir/nu0.mgz
set numnc = /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
if ( $DoAntsN3 ) then
if ( 0 ) then
if ( $DoAntsN4 ) then
if ( 1 ) then
set cmd = ( AntsN4BiasFieldCorrectionFs -i $InVol -o $numnc )
set cmd = ( AntsN4BiasFieldCorrectionFs -i orig.mgz -o
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz )
if ( $#MaskVol ) set cmd = ( $cmd -x $MaskVol )
if ( 0 ) set cmd = ( AntsN4BiasFieldCorrectionFs -i orig.mgz -o
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz -x )
endif
endif
echo "cd `pwd`" | tee -a $LF
echo cd `pwd`
tee -a ./mri_nu_correct.mni.log
pwd
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
echo $cmd | tee -a $LF
echo AntsN4BiasFieldCorrectionFs -i orig.mgz -o
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
tee -a ./mri_nu_correct.mni.log
AntsN4BiasFieldCorrectionFs -i orig.mgz -o
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
$cmd | & tee -a $LF
AntsN4BiasFieldCorrectionFs -i orig.mgz -o
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
tee -a ./mri_nu_correct.mni.log
Using shrink factor: 4
if ( $status ) exit 1 ;
if ( 0 ) exit 1
else
else
if ( $DoRescale ) then
if ( 1 ) then
set ones = $tmpdir/ones.mgz
set ones = /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
set cmd = ( mri_binarize --i $numnc --min -1 --o $ones ) ;
set cmd = ( mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
--min -1 --o /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz )
echo $cmd | tee -a $LF
echo mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --min -1
--o /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
tee -a ./mri_nu_correct.mni.log
mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --min -1 --o
/dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
$cmd | tee -a $LF
mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --min -1 --o
/dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
tee -a ./mri_nu_correct.mni.log
7.1.1
cwd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --min
-1 --o /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
sysname Linux
hostname HEUBME.com
machine x86_64
user liubing
input /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
frame 0
nErode3d 0
nErode2d 0
output /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777215 voxels in final mask
Count: 16777215 16777215.000000 16777216 99.999994
mri_binarize done
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set cmd = ( mri_segstats --id 1 --seg $ones --i $InVol --sum $tmpdir/sum.junk
--avgwf $tmpdir/input.mean.dat )
set cmd = ( mri_segstats --id 1 --seg
/dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i orig.mgz --sum
/dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/input.mean.dat )
echo $cmd | tee -a $LF
echo mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
--i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/input.mean.dat
tee -a ./mri_nu_correct.mni.log
mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i
orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/input.mean.dat
$cmd | tee -a $LF
mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i
orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/input.mean.dat
tee -a ./mri_nu_correct.mni.log
7.1.1
cwd
cmdline mri_segstats --id 1 --seg
/dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i orig.mgz --sum
/dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/input.mean.dat
sysname Linux
hostname HEUBME.com
machine x86_64
user liubing
whitesurfname white
UseRobust 0
Loading /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to /dev/shm/tmp.mri_nu_correct.mni.2576084/input.mean.dat
mri_segstats done
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set inmean = `cat $tmpdir/input.mean.dat`
set inmean = `cat $tmpdir/input.mean.dat`
cat /dev/shm/tmp.mri_nu_correct.mni.2576084/input.mean.dat
set cmd = ( mri_segstats --id 1 --seg $ones --i $numnc --sum $tmpdir/sum.junk
--avgwf $tmpdir/output.mean.dat )
set cmd = ( mri_segstats --id 1 --seg
/dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --sum
/dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/output.mean.dat )
echo $cmd | tee -a $LF
echo mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
--i /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --sum
/dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/output.mean.dat
tee -a ./mri_nu_correct.mni.log
mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --sum
/dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/output.mean.dat
$cmd | tee -a $LF
mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --sum
/dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/output.mean.dat
tee -a ./mri_nu_correct.mni.log
7.1.1
cwd
cmdline mri_segstats --id 1 --seg
/dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz --i
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz --sum
/dev/shm/tmp.mri_nu_correct.mni.2576084/sum.junk --avgwf
/dev/shm/tmp.mri_nu_correct.mni.2576084/output.mean.dat
sysname Linux
hostname HEUBME.com
machine x86_64
user liubing
whitesurfname white
UseRobust 0
Loading /dev/shm/tmp.mri_nu_correct.mni.2576084/ones.mgz
Loading /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to /dev/shm/tmp.mri_nu_correct.mni.2576084/output.mean.dat
mri_segstats done
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set outmean = `cat $tmpdir/output.mean.dat`
set outmean = `cat $tmpdir/output.mean.dat`
cat /dev/shm/tmp.mri_nu_correct.mni.2576084/output.mean.dat
set scale = `echo $inmean/$outmean | bc -l`
set scale = `echo $inmean/$outmean | bc -l`
bc -l
echo 22.21392/14.24947
Missing parameters.
Usage:
bc inputImageFile inputSegmentationFile side PathToTrainingFiles
outputSegmentationFile
side = 0 (left side) or else (right side)
set cmd = ( mris_calc -o $numnc $numnc mul $scale )
set cmd = ( mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz mul )
echo $cmd | tee -a $LF
echo mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz mul
tee -a ./mri_nu_correct.mni.log
mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz mul
$cmd | tee -a $LF
mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.2576084/nu0.mgz mul
tee -a ./mri_nu_correct.mni.log
Segmentation fault (core dumped)
if ( $status ) exit 1 ;
if ( 139 ) exit 1
exit 1
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Freesurfer@nmr.mgh.harvard.edu
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