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The killed part is unrelated to the first error (which has no impact on the FreeSurfer outputs as far as I know). Killed means your job was killed externally by something or someone. If you are running your job on a cluster that has time limits on particular
queues, that might be what got triggered. Another possibility is that your sysadmin is dissatisfied with you (so you should discuss with them about this).
Peace,
Matt.
From: Dr Sampada Sinha <[email protected]>
Date: Wednesday, February 18, 2015 at 2:15 PM To: "[email protected]" <[email protected]> Subject: [HCP-Users] Regarding: (standard_in) 2: Error: comparison in expressionSourcing AFNI to run my resting state python script Dear HCP team members,
I am really sorry to bother you all again, but during running of recon-all command I am repeatedly getting this error:
(standard_in) 2: Error: comparison in _expression_
/home/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: line 80: 29951 Killed mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz "$SubjectDIR"/"$SubjectID"/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca
"$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta
When I checked the output file no error was found (I have attached the output file with this mail)
I saw Dr Matthew's post on freesurfer archives for the same problem (05/18/2012) and he said getopt (used in fsl-sub) doesn't work correctly when this flag is not set to 1 and it is better to set it to 0.
Will you please let me know where do I make the change and what do I change it to?
I am really sorry for putting up questions so many times but will greatly appreciate if I can get any answer regarding this.
Much thanks for your patience and time...
Regards,
Sampada
Sampada Sinha
Post-Doctoral Associate
University of Minnesota (East Bank)
Molecular and neuroimaging laboratory
Department of Psychiatry
Minneapolis-55415
Phone number: 718-913-0636
email: [email protected]
_______________________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ |
- [HCP-Users] Regarding: (standard_in) 2: Error: comparison... Dr Sampada Sinha
- Re: [HCP-Users] Regarding: (standard_in) 2: Error: c... Glasser, Matthew
- Re: [HCP-Users] Regarding: (standard_in) 2: Erro... Kevin Archie
