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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
