Hi Doug,

I am running preprocessing on freesurfer 5.1 using this line:

preproc-sess -s 121210_xu_Object4catmod_10 -df sessdir -per-run -sliceorder siemens -fsd bold  -fwhm 0 -mni305-2mm -surface self lhrh  -force

and I get a "Segmentation fault " error. Here is part of the output with the error:

....
mri_segreg --mov bold/007/tmp.bbregister.28256/template.nii --init-reg bold/007/tmp.bbregister.28256/reg.init.dat --out-reg bold/007/tmp.bbregister.28256/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $
setenv SUBJECTS_DIR /ncf/vcn/Maryam/mri-space/subjects
cd /ncf/vcn/Maryam/mri-space/studies/Obj4cat_mod/unpackdata/121210_xu_Object4catmod_10
mri_segreg --mov bold/007/tmp.bbregister.28256/template.nii --init-reg bold/007/tmp.bbregister.28256/reg.init.dat --out-reg bold/007/tmp.bbregister.28256/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 
sysname  Linux
hostname ncfws09.rc.fas.harvard.edu
machine  x86_64
user     mvpashkam
movvol bold/007/tmp.bbregister.28256/template.nii
regfile bold/007/tmp.bbregister.28256/reg.init.dat
subject green_alligator_kcb
dof 6
outregfile bold/007/tmp.bbregister.28256/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1358526945
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 1.000  -0.007   0.027  -1.374;
-0.026   0.032   0.999  -28.956;
 0.008   0.999  -0.032   7.006;
 0.000   0.000   0.000   1.000;

Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Segmentation fault 


I have attached the full log file. I am not sure where the problem is. The anatomical data of the subject has been analyzed using recon all on freesurfer 4.5. I have used similar method for 9 other subjects and there was no error on any of them before. Any idea why am I getting a segmentation error?

Thanks,
Maryam