Log file is provantreg.dat.log jue jul 28 09:47:50 CEST 2016 setenv SUBJECTS_DIR ./lesresos cd /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis /usr/local/freesurfer/bin/bbregister --s SUBJ_ID --mov ./allpets/SUBJ_ID/SUBJ_ID_PETFBP.nii.gz --reg provantreg.dat --init-fsl --t1 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID_PETFBP.nii.gz ./tmp.bbregister.3775/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID_PETFBP.nii.gz ./tmp.bbregister.3775/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./allpets/SUBJ_ID/SUBJ_ID_PETFBP.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to ./tmp.bbregister.3775/template.nii... fslregister --s SUBJ_ID --mov ./tmp.bbregister.3775/template.nii --reg ./tmp.bbregister.3775/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.3775/fslregister --dof 6 Log file is ./tmp.bbregister.3775/reg.init.dat.fslregister.log jue jul 28 09:47:50 CEST 2016 --s SUBJ_ID --mov ./tmp.bbregister.3775/template.nii --reg ./tmp.bbregister.3775/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.3775/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ fredlab Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis mri_convert ./lesresos/SUBJ_ID/mri/brainmask.mgz ./tmp.bbregister.3775/fslregister/refvol.fslregister.nii mri_convert ./lesresos/SUBJ_ID/mri/brainmask.mgz ./tmp.bbregister.3775/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./lesresos/SUBJ_ID/mri/brainmask.mgz... TR=8.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.84288e-08, 1.13621e-07) j_ras = (1.22935e-07, 3.84171e-09, -1) k_ras = (-1.52737e-07, 1, -5.82078e-09) writing to ./tmp.bbregister.3775/fslregister/refvol.fslregister.nii... -------------------------------------- /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis mri_convert ./tmp.bbregister.3775/template.nii ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.3775/template.nii ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.3775/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii... Mov determinant is -8 /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis tkregister2_cmdl --mov ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.3775/fslregister/reg0.3810.dat --regheader --fslregout ./tmp.bbregister.3775/reg.init.dat.fsl.mat0 --s SUBJ_ID --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.3775/fslregister/reg0.3810.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target ./lesresos/SUBJ_ID/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -89.000; 0.000 -2.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 6.490; -0.000 -0.000 1.000 -7.940; 0.000 -1.000 0.000 -22.114; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 6.490; -0.000 -0.000 1.000 -7.940; 0.000 -1.000 0.000 -22.114; 0.000 0.000 0.000 1.000; Determinant 1 subject = SUBJ_ID RegMat --------------------------- 1.000 -0.000 -0.000 6.490; -0.000 -0.000 1.000 -7.940; 0.000 -1.000 0.000 -22.114; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 jue jul 28 09:47:52 CEST 2016 /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis flirt.fsl -ref ./tmp.bbregister.3775/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.3775/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.3775/reg.init.dat.fsl.mat0 jue jul 28 09:48:07 CEST 2016 /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis flirt.fsl -ref ./tmp.bbregister.3775/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.3775/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.3775/reg.init.dat.fsl.mat -init ./tmp.bbregister.3775/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s SUBJ_ID --mov ./tmp.bbregister.3775/template.nii --reg ./tmp.bbregister.3775/reg.init.dat --fslreg ./tmp.bbregister.3775/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.997 -0.029 -0.076 12.815; -0.073 0.098 -0.992 187.765; 0.036 0.995 0.096 -16.440; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.3775/template.nii reg file ./tmp.bbregister.3775/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target ./lesresos/SUBJ_ID/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./tmp.bbregister.3775/template.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -89.000; 0.000 -2.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8, ref det = -1 ---- Input registration matrix (computed) -------- 0.997 -0.036 -0.073 3.655; 0.076 0.096 0.992 -24.593; -0.029 -0.995 0.098 -6.508; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.997 -0.036 -0.073 3.655; 0.076 0.096 0.992 -24.593; -0.029 -0.995 0.098 -6.508; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = SUBJ_ID RegMat --------------------------- 0.997 -0.036 -0.073 3.655; 0.076 0.096 0.992 -24.593; -0.029 -0.995 0.098 -6.508; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: _ (standard_in) 1: syntax error Started at jue jul 28 09:47:50 CEST 2016 Ended at jue jul 28 09:48:35 CEST 2016 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.3775/template.nii --reg ./tmp.bbregister.3775/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.3775/template.nii --init-reg ./tmp.bbregister.3775/reg.init.dat --out-reg ./tmp.bbregister.3775/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 --wm-gt-gm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR ./lesresos cd /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis mri_segreg --mov ./tmp.bbregister.3775/template.nii --init-reg ./tmp.bbregister.3775/reg.init.dat --out-reg ./tmp.bbregister.3775/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 --wm-gt-gm 0.5 sysname Linux hostname fredlab machine x86_64 user fred movvol ./tmp.bbregister.3775/template.nii regfile ./tmp.bbregister.3775/reg.init.dat subject SUBJ_ID dof 6 outregfile ./tmp.bbregister.3775/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 1470691423 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.997 -0.036 -0.073 3.655; 0.076 0.096 0.992 -24.593; -0.029 -0.995 0.098 -6.508; 0.000 0.000 0.000 1.000; Segmentation fault (core dumped)