My first suspect would be the dread Linux out-of-memory killer. Are you sure you have enough RAM for this?
- Kevin > On Feb 18, 2015, at 2:19 PM, Glasser, Matthew <[email protected]> wrote: > > 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] > <mailto:[email protected]>> > Date: Wednesday, February 18, 2015 at 2:15 PM > To: "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[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] <mailto:email%[email protected]> > [email protected] <mailto:[email protected]> > > > > > > > > > _______________________________________________ > HCP-Users mailing list > [email protected] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > > 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 mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
