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.
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
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" dgreve@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 Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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" <dgreve@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 listFreesurfer@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
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" <dgreve@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 listFreesurfer@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
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" dgreve@MGH.HARVARD.EDU 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" dgreve@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 Freesurfer@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-AhxHsn6nFRaiABYGIwTWlprmPaq...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
liub