External Email - Use Caution Yes, I first ran autorecon1 and 2 for the initial processing. I then made only made brainmask edits followed by running it with autorecon2. The thing is that according to this URL
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable > The ribbon.mgz is created in autorecon3, for this reason the file does not exist. So why is it being called autorecon2? On Fri, Jul 13, 2018 at 5:27 PM Glasser, Matthew <glass...@wustl.edu> wrote: > External Email - Use Caution > > Did you run the preceding steps of FreeSurfer? Does that file exist? > > Peace, > > Matt. > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Aaron > Tanenbaum <aaron.b.tanenb...@gmail.com> > Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu> > Date: Friday, July 13, 2018 at 5:24 PM > To: Freesurfer <Freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] missing ribbon.mgz > > External Email - Use Caution > > I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I am > getting an error, see below > I am using the command > > recon-all -s BOLD-52_v1 -mprage -autorecon2 > This has happened before. What did I do wrong. > > > > #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018 >> >> INFO: mri_segstats will not calculate Supratentorial >> due to missing ribbon.mgz file >> /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1 >> >> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz >> --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 >> --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm >> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray >> --euler --ctab /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt >> --subject BOLD-52_v1 >> >> >> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >> cwd >> cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv >> mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg >> --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz >> --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol >> --surf-ctx-vol --totalgray --euler --ctab >> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject >> BOLD-52_v1 >> sysname Linux >> hostname brahms >> machine x86_64 >> user tanenbauma >> UseRobust 0 >> atlas_icv (eTIV) = 1714974 mm^3 (det: 1.135939 ) >> mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz, >> -1): could not open file >> Computing euler number >> orig.nofix lheno = -70, rheno = -38 >> orig.nofix lhholes = 36, rhholes = 20 >> Loading mri/aseg.mgz >> Getting Brain Volume Statistics >> Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07 >> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > > > > > > ------------------------------ > > 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. > _______________________________________________ > 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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