External Email - Use Caution 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. > >
_______________________________________________ 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.
