Hi Doug, That file does not exist, because none of the surf files got created from this pipeline. So there was an error before that?
The mri files got created (partially) and what's there looks good. Missing are: aseg.mgz, aparc.a2009s+aseg.mgz, aparc+aseg.mgz, aseg.auto.noCCseg.mgz, aseg.auto.mgz, brain.mgz, brain.finalsurfs.mgz, lh.ribbon.mgz, rh.ribbon.mgz, filled.mgz, wm.mgz, wm.seg.mgz There is plenty of memory here on the server. But is this maybe an issue with job timing out of server? Otherwise memory and space not an issue. Any help appreciated. Thank you, Anvi > On May 25, 2015, at 6:38 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > The error says: > > mris_fix_topology: could not read input surface > /sc/orga/projects/psychimage/MCIC/Schizophrenia/SiteC/Cooked/A00036129/Freesurfer/A00036129/surf/lh.qsphere.nofix > No such file or directory > > Does that file exist? Have you run out of disc space on that volume? > > doug > > >> On 5/22/15 8:11 PM, anvi vora wrote: >> Hello, >> >> So recon-all seems to be running on my Mac fine, with this same data. But >> it does not run on my institution's Minerva linux server. >> >> It did most of volumetric processing steps, but failed on surface processing >> steps, and then all of the rest. >> >> I have checked that environment variables are correct, and they are I >> believe. >> >> Attached is the entire recon-all.log file >> >> I will appreciate any help! >> >> Thank you very much, >> Anvi >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > 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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