On Tue, Apr 16, 2013 at 1:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Miklos, did you run all the steps that go before autorecon2?
doug

On 04/16/2013 12:23 PM, Miklos Argyelan wrote:
> Hi,
>
> I have recently installed Freesurfer on a new computer, and downloaded
> the latest version of Freesurfer (centos 64 bit) and when ran:
>
> recon-all -subject test001 -autorecon2
>
> I got the following error message:
>
> $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
> /usr/local/freesurfer/ASegStatsLUT.txt --subject test001
> sysname Linux
> hostname mikbox
> machine x86_64
> user amiklos
> UseRobust 0
> atlas_icv (eTIV) = 1444225 mm^3 (det: 1.348893 )

> *mghRead(/home/amiklos/nethome/work/METHODS/FS/subjects/test001/mri/ribbon.mgz,
> -1): could not open file*

>
> I am not sure but the bug seems that autorecon2 tries to run SegStats
> too early (supposed to be in autorecon3).
>
> Maybe this is the error in recon-all:
> case "-autorecon2":
> set DoGCAReg = 1;
> set DoCARegInv = 1;
> set DoRemoveNeck = 1;
> set DoSkullLTA = 1;
> set DoCANormalize = 1;
> set DoCAReg = 1;
> set DoCALabel = 1;

> *set DoSegStats = 1;*

> set DoNormalization2 = 1;
> set DoMaskBFS = 1;
> set DoSegmentation = 1;
> set DoFill = 1;
> set DoTessellate = 1;
> set DoSmooth1 = 1;
> set DoInflate1 = 1;
> set DoQSphere = 1;
> set DoFix = 1;
> set DoSmooth2 = 1;
> set DoInflate2 = 1;
> set DoWhiteSurfs = 1;
> set DoCurvStats = 1;
> breaksw
>
> Could some expert verify please that this is indeed the problem and I
> can change the 1 to zero, or am I completely off?
>
> Miklos
>
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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