External Email - Use Caution
Did you run the preceding steps of FreeSurfer? Does that file exist?
Peace,
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> Date: Friday, July 13, 2018 at 5:24 PM To: Freesurfer <Freesurfer@nmr.mgh.harvard.edumailto: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
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