Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)
External Email - Use Caution Yeah,you are right! The prolem has been solved after modifying the 'bc' path. Thank you very much! Have a good day :)! -原始邮件- 发件人:"Douglas N. Greve" 发送时间:2021-06-02 05:52:10 (星期三) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped) Actually, I think I see what the problem is. You apparently have a command called "bc" in your path. mri_nu_correct.mni is trying to use the linux-native bc command (a simple calculator usually located in /bin). What do you get when you run which bc On 6/1/2021 9:59 AM, liub wrote: 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" 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.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1B5w2wF5qwtbUrPtw-T-AhxHsn6nFRaiABYGIwTWlprmPaq6YiwiBPcsu9d72mLiNviRyhNO5nYHnfhC4BUWrTBJP6OKL2r5K1-1lJ7xu6LLiHfOgOG9lfic2WKaGPa7aqyT-R2b4BIFo5jk0HGbx_b8_1SzR1UhMjJoY9O7xFrIqtvUe6ze2h9Jh5WuHvnbtGp4pJMzyTbeG2y8x6jwNuNnWR54_2fBc3ZpfR8IUEz9i9o9DwQK0eS84FG3TGjzT26m4GZoHoJzvZi03umKrEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)
Actually, I think I see what the problem is. You apparently have a command called "bc" in your path. mri_nu_correct.mni is trying to use the linux-native bc command (a simple calculator usually located in /bin). What do you get when you run which bc On 6/1/2021 9:59 AM, liub wrote: 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" *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 listfreesur...@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)
What happens when you run the following two commands? echo 5/6 | bc -l echo "5/6" | bc -l On 6/1/2021 9:59 AM, liub wrote: 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" *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 listfreesur...@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)
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" 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
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
