recon-all -autorecon2 bug? - Freesurfer

16 Apr 2013


      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