Dear freesurfer community,

unfortunately there was a mistake in the previous mail.

Please find attached the current valid mail and ignore previous mail from my adress.

Dear freesurfer community,

We are conducting cortical-thickness analysis using freesurfer 5.3.0 and have been experiencing problems with the computation after eliminating dura mater and optical nerve.

For several subjects we ran the command “recon-all –autorecon2 –subjid XXXX_mdeft.” and received the error message “mri_segstats will not calculate Supratentorial due to missing

ribbon.mgz file”.

Below, we provide the details of our setup and the exact error message for one subject.

Feel free to ask for more information. Thank you very much for your help!

Yours sincerely,

Jana Dinges

FREESURFER_HOME: /apps/prod/i486/freesurfer-5.3.0

Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

Debian version: 5.0.6

Kernel info: Linux 2.6.27.39-1-ql-beowulf i686

$ which freesurfer -> /apps/prod/i486/freesurfer-5.3.0/bin/freesurfer

Used command:

recon-all –autorecon2 –subjid BB53_mdeft.

Error Message:

INFO: mri_segstats will not calculate Supratentorial
due to missing ribbon.mgz file
/data/projects/oertelmatura/Neurodegeneration_MCI/BB53_mdeft.

mri_segstats—seg mri/aseg.mgz—sum stats/aseg.stats—pv mri/norm.mgz—empty—brainmask mri/brainmask.mgz—brain-e norm—in-intensity-units MR—etiv—surf-wm-vol—surf-ctx-vol—totalgray—euler—ctab /apps/prod/x86_64/freesurf

$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 -ity-name norm—in-intensity-units MR—etiv—surf-wm-vol—surf-ctx-vol—totalgray—euler—ctab /apps/prod/x86_64/f
sysname Linux
hostname beo-05
machine x86_64
user     jdinges
UseRobust 0
atlas_icv (eTIV) = 1723578 mm^3    (det: 1.130268 )
mghRead(/data/projects/oertelmatura/Neurodegeneration_MCI/BB53_mdeft./mri/ribbon.mgz, -1): could not open file
Computing euler number
orig.nofix lheno = -70, rheno = -38
orig.nofix lhholes =   36, rhholes = 20
--
Getting Brain Volume Statistics
Linux beo-05 2.6.32.59-ql-beowulf-54 #1 SMP Fri Nov 2 12:47:48 CET 2012 x86_64 GNU/Linux

recon-all -s BB53_mdeft. exited with ERRORS at Fri Nov 1 03:55:37 CET 2013