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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