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I just noticed that this problem is a now and resolved. I just have to replace the mri_segstats. Thank you for your time.
On Fri, Jul 13, 2018 at 6:08 PM Aaron Tanenbaum aaron.b.tanenbaum@gmail.com wrote:
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
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 glasserm@wustl.edu wrote:
External Email - Use CautionDid you run the preceding steps of FreeSurfer? Does that file exist?
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Aaron Tanenbaum aaron.b.tanenbaum@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 CautionI 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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