External Email - Use Caution on the log it says that cpu time is unlimited.
On Thu, Aug 2, 2018 at 12:58 PM, Ortal Nakash <ortal...@sas.upenn.edu> wrote: > Do you mean that I should have used higher memory? > > Is there a way to continue running it from where it stopped or should I > start it all over again? > > On the Freesurfer Archive there's a suggestion to use the following > command: recon-all -make all -s <subjid> However, when I tried it gave an > error; *ERROR: cannot find /share/apps/freesurfer/6.0.0/subjects/103T.* > > > On Thu, Aug 2, 2018 at 12:49 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> hmmm, it looks like it just stopped in the middle of a process. DId it >> exceed some wall time limit perhaps? >> >> On Thu, 2 Aug 2018, Ortal Nakash wrote: >> >> >>> External Email - Use Caution >>> >>> Sure, here it is. >>> >>> On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> wrote: >>> can you send it as a text file (not converted to .docx)? >>> On Thu, 2 Aug 2018, Ortal Nakash wrote: >>> >>> >>> External Email - Use Caution >>> >>> I copied it in the attached file. >>> Thank you, >>> Ortal >>> >>> On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Ortal >>> >>> you need to send us the recon-all.log, otherwise we >>> don't have the >>> information we need >>> to help you >>> >>> cheers >>> Bruce >>> On Thu, 2 Aug 2018, Ortal Nakash wrote: >>> >>> >>> External Email - Use Caution >>> >>> Hi, >>> >>> I tried to run the recon-all command on a single >>> participant on >>> a high >>> memory cluster by typing: >>> >>> qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G >>> >>> >>> recon-all -i 103_T1.nii.gz -s 103T -sd >>> /data/jag/cnds/ortal/freesurftest/C103/ -all >>> >>> >>> - Most of the necessary files were created, >>> however the >>> aparc.a2009 files >>> and the recon-all.done >>> file were not. >>> >>> >>> sincerely, >>> >>> Ortal Nakash >>> >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >>> >> _______________________________________________ >> 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. >> >> >
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