Dear FreeSurfer Experts,
I have just launched a new project and collected new T1 weighted images (as my previous ones) and started processing them using FreeSurfer. Unfortunaely non of them works with FreeSurfer. When I run recon-all -autorecon-all -s subjecname, I get the following error:
#@# Talairach Fri Oct 6 09:20:02 EEST 2017 /home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s mcropped_noor exited with ERRORS at Fri Oct 6 09:20:05 EEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I have checked my images and they look fine and they are similar to the ones I have processed a year ago.
I have searched for a solution to this error but unfortunately I did not find any. Could you please help me on this?
Thanks alot in advance,
Ali
Hi Ali
can you send us your full command line, the full screen output and the recon-all.log file that should have been generated in the subject's scripts dir?
cheers Bruce On Fri, 6 Oct 2017, Ali Radaideh wrote:
Dear FreeSurfer Experts,
I have just launched a new project and collected new T1 weighted images (as my previous ones) and started processing them using FreeSurfer. Unfortunaely non of them works with FreeSurfer. When I run recon-all -autorecon-all -s subjecname, I get the following error:
#@# Talairach Fri Oct 6 09:20:02 EEST 2017 /home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s mcropped_noor exited with ERRORS at Fri Oct 6 09:20:05 EEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I have checked my images and they look fine and they are similar to the ones I have processed a year ago.
I have searched for a solution to this error but unfortunately I did not find any. Could you please help me on this?
Thanks alot in advance,
Ali
-- Ali M. Al-Radaideh. PhD Department of Medical Imaging Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
Dear Bruce,
many thanks for your email. I have noticed that the FreeSurfer I am still using is 5.3.0 and this version seems not to work with my Ubuntu 16.10 due to issues related to the current version of "Perl" (version 22). I have just downloaded the latest version of FreeSurfer (version 6) and everything seems to work fine.
Many thanks, Ali
On Fri, Oct 6, 2017 at 4:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ali
can you send us your full command line, the full screen output and the recon-all.log file that should have been generated in the subject's scripts dir?
cheers Bruce On Fri, 6 Oct 2017, Ali Radaideh wrote:
Dear FreeSurfer Experts,
I have just launched a new project and collected new T1 weighted images (as my previous ones) and started processing them using FreeSurfer. Unfortunaely non of them works with FreeSurfer. When I run recon-all -autorecon-all -s subjecname, I get the following error:
#@# Talairach Fri Oct 6 09:20:02 EEST 2017 /home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s mcropped_noor exited with ERRORS at Fri Oct 6 09:20:05 EEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting
I have checked my images and they look fine and they are similar to the ones I have processed a year ago.
I have searched for a solution to this error but unfortunately I did not find any. Could you please help me on this?
Thanks alot in advance,
Ali
-- Ali M. Al-Radaideh. PhD Department of Medical Imaging Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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 Partners Compliance HelpLine at http://www.partners.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.
glad to hear it worked out Bruce On Sat, 7 Oct 2017, Ali Radaideh wrote:
Dear Bruce,
many thanks for your email. I have noticed that the FreeSurfer I am still using is 5.3.0 and this version seems not to work with my Ubuntu 16.10 due to issues related to the current version of "Perl" (version 22). I have just downloaded the latest version of FreeSurfer (version 6) and everything seems to work fine.
Many thanks, Ali
On Fri, Oct 6, 2017 at 4:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ali
can you send us your full command line, the full screen output and the recon-all.log file that should have been generated in the subject's scripts dir? cheers Bruce On Fri, 6 Oct 2017, Ali Radaideh wrote: Dear FreeSurfer Experts, I have just launched a new project and collected new T1 weighted images (as my previous ones) and started processing them using FreeSurfer. Unfortunaely non of them works with FreeSurfer. When I run recon-all -autorecon-all -s subjecname, I get the following error: #@# Talairach Fri Oct 6 09:20:02 EEST 2017 /home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mcropped_noor exited with ERRORS at Fri Oct 6 09:20:05 EEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have checked my images and they look fine and they are similar to the ones I have processed a year ago. I have searched for a solution to this error but unfortunately I did not find any. Could you please help me on this? Thanks alot in advance, Ali -- Ali M. Al-Radaideh. PhD Department of Medical Imaging Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.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.-- Ali M. Al-Radaideh. PhD Department of Medical Imaging Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
freesurfer@nmr.mgh.harvard.edu
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Ali Radaideh -
Bruce Fischl