I have put patches for mri_segstats here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/

this should fix the problem

doug

On 11/3/13 12:09 PM, jana dinges wrote:

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

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