Hi Maryam, can you verify that the rh surfaces for that subject are ok? Load rh.white with rh.thickness as an overlay doug
On 01/09/2013 05:31 PM, Maryam Vaziri Pashkam wrote:
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 http://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