Logfile for bbregister Mon Aug 24 17:10:21 EDT 2009 setenv SUBJECTS_DIR /autofs/space/lang_012/users/CVRAM cd /autofs/space/orion_002/users/DTI/SCRIPTS /usr/local/freesurfer/dev/bin/bbregister --s CVRAM_1046_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --dti --init-fsl --reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/CVRAM_1046_lowb-to-anat.reg $Id: bbregister,v 1.30 2009/08/07 22:20:40 greve Exp $ Linux compute-0-54.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii mri_convert /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii $Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $ reading from /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 0) j_ras = (0, 1, 7.45058e-09) k_ras = (-7.45058e-09, -7.45058e-09, 1) writing to /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii... fslregister --s CVRAM_1046_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister --dof 6 Log file is /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fslregister.log Mon Aug 24 17:10:22 EDT 2009 --s CVRAM_1046_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister --dof 6 $Id: fslregister,v 1.29 2009/07/31 22:22:46 greve Exp $ compute-0-54.local Linux compute-0-54.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/space/orion_002/users/DTI/SCRIPTS mri_convert /autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/mri/brainmask.mgz /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii mri_convert /autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/mri/brainmask.mgz /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $ reading from /autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/mri/brainmask.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 6.48571e-10, -2.03171e-09) j_ras = (-6.45517e-09, 1.95524e-10, -1) k_ras = (-2.3879e-10, 1, -6.07039e-10) writing to /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/space/orion_002/users/DTI/SCRIPTS mri_convert /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii --frame 0 mri_convert /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $ reading from /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 0) j_ras = (0, 1, 7.45058e-09) k_ras = (-7.45058e-09, -7.45058e-09, 1) keeping frame 0 writing to /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii... /autofs/space/orion_002/users/DTI/SCRIPTS tkregister2_cmdl --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/reg0.27601.dat --regheader --fslregout /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat0 --s CVRAM_1046_recon --noedit tkregister_tcl /usr/local/freesurfer/dev/lib/tcl/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii reg file /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/reg0.27601.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.108 2009/04/02 17:14:46 mreuter Exp $ Diagnostic Level -1 INFO: loading target /autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/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 /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -60.000; 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 -3.668; 0.000 -0.000 1.000 -25.734; -0.000 -1.000 -0.000 -3.235; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 0.000 -3.668; 0.000 -0.000 1.000 -25.734; -0.000 -1.000 -0.000 -3.235; 0.000 0.000 0.000 1.000; Determinant 1 subject = CVRAM_1046_recon RegMat --------------------------- 1.000 -0.000 0.000 -3.668; 0.000 -0.000 1.000 -25.734; -0.000 -1.000 -0.000 -3.235; 0.000 0.000 0.000 1.000; register: file /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/reg0.27601.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 Mon Aug 24 17:10:26 EDT 2009 /autofs/space/orion_002/users/DTI/SCRIPTS flirt -ref /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii -in /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii -bins 256 -omat /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -schedule /usr/local/freesurfer/dev/bin/flirt.newdefault.20080811.sch -init /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat0 tkregister2_cmdl --s CVRAM_1046_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat --fslreg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/dev/lib/tcl/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.009 -0.004 -3.309; -0.004 0.003 -1.000 162.838; 0.009 1.000 0.003 -4.390; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii reg file /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.108 2009/04/02 17:14:46 mreuter Exp $ Diagnostic Level -1 INFO: loading target /autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/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 /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -60.000; 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) -------- 1.000 -0.009 -0.004 -4.609; 0.004 0.003 1.000 -25.289; -0.009 -1.000 0.003 -3.122; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.009 -0.004 -4.609; 0.004 0.003 1.000 -25.289; -0.009 -1.000 0.003 -3.122; 0.000 0.000 0.000 1.000; Determinant 1 subject = CVRAM_1046_recon RegMat --------------------------- 1.000 -0.009 -0.004 -4.609; 0.004 0.003 1.000 -25.289; -0.009 -1.000 0.003 -3.122; 0.000 0.000 0.000 1.000; register: file /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat written (standard_in) 1: illegal character: V (standard_in) 1: illegal character: R (standard_in) 1: parse error (standard_in) 1: illegal character: M (standard_in) 1: illegal character: _ (standard_in) 1: illegal character: _ Started at Mon Aug 24 17:10:23 EDT 2009 Ended at Mon Aug 24 17:10:52 EDT 2009 fslregister Done To check results, run: tkregister2 --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat --surf orig mri_segreg --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii --init-reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat --out-reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.84 2009/07/21 14:15:11 fischl Exp $ setenv SUBJECTS_DIR /autofs/space/lang_012/users/CVRAM cd /autofs/space/orion_002/users/DTI/SCRIPTS mri_segreg --mov /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii --init-reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat --out-reg /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname compute-0-54.local machine x86_64 user tori movvol /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii regfile /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat subject CVRAM_1046_recon dof 6 outregfile /autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/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 DoPowell 1 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1251425381 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.009 -0.004 -4.609; 0.004 0.003 1.000 -25.289; -0.009 -1.000 0.003 -3.122; 0.000 0.000 0.000 1.000; Loading mov Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting LH Surfs Projecting RH Surfs Loading rh.white surf Loading rh.thickness *** glibc detected *** mri_segreg: free(): invalid next size (normal): 0x000000002daf0d40 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3e42e6f4f4] /lib64/libc.so.6(cfree+0x8c)[0x3e42e72b1c] mri_segreg[0x433c1e] mri_segreg[0x433e3d] mri_segreg[0x42d1a3] mri_segreg(vfprintf+0x2b08)[0x40c490] mri_segreg(vfprintf+0x3253)[0x40cbdb] mri_segreg[0x40f6a7] /lib64/libc.so.6(__libc_start_main+0xf4)[0x3e42e1d8a4] mri_segreg(__gxx_personality_v0+0x172)[0x40abfa] ======= Memory map: ======== 00400000-00adc000 r-xp 00000000 00:1f 2868262 /autofs/space/freesurfer/centos4.0_x86_64/dev/bin/mri_segreg 00bdc000-00c61000 rw-p 006dc000 00:1f 2868262 /autofs/space/freesurfer/centos4.0_x86_64/dev/bin/mri_segreg 00c61000-02423000 rw-p 00c61000 00:00 0 1b95a000-2db11000 rw-p 1b95a000 00:00 0 3e42a00000-3e42a1a000 r-xp 00000000 08:02 14291920 /lib64/ld-2.5.so 3e42c19000-3e42c1a000 r--p 00019000 08:02 14291920 /lib64/ld-2.5.so 3e42c1a000-3e42c1b000 rw-p 0001a000 08:02 14291920 /lib64/ld-2.5.so 3e42e00000-3e42f46000 r-xp 00000000 08:02 14291921 /lib64/libc-2.5.so 3e42f46000-3e43146000 ---p 00146000 08:02 14291921 /lib64/libc-2.5.so 3e43146000-3e4314a000 r--p 00146000 08:02 14291921 /lib64/libc-2.5.so 3e4314a000-3e4314b000 rw-p 0014a000 08:02 14291921 /lib64/libc-2.5.so 3e4314b000-3e43150000 rw-p 3e4314b000 00:00 0 3e43200000-3e43202000 r-xp 00000000 08:02 14291922 /lib64/libdl-2.5.so 3e43202000-3e43402000 ---p 00002000 08:02 14291922 /lib64/libdl-2.5.so 3e43402000-3e43403000 r--p 00002000 08:02 14291922 /lib64/libdl-2.5.so 3e43403000-3e43404000 rw-p 00003000 08:02 14291922 /lib64/libdl-2.5.so 3e43600000-3e43615000 r-xp 00000000 08:02 14291926 /lib64/libpthread-2.5.so 3e43615000-3e43814000 ---p 00015000 08:02 14291926 /lib64/libpthread-2.5.so 3e43814000-3e43815000 r--p 00014000 08:02 14291926 /lib64/libpthread-2.5.so 3e43815000-3e43816000 rw-p 00015000 08:02 14291926 /lib64/libpthread-2.5.so 3e43816000-3e4381a000 rw-p 3e43816000 00:00 0 3e44200000-3e44282000 r-xp 00000000 08:02 14291700 /lib64/libm-2.5.so 3e44282000-3e44481000 ---p 00082000 08:02 14291700 /lib64/libm-2.5.so 3e44481000-3e44482000 r--p 00081000 08:02 14291700 /lib64/libm-2.5.so 3e44482000-3e44483000 rw-p 00082000 08:02 14291700 /lib64/libm-2.5.so 3e44a00000-3e44a14000 r-xp 00000000 08:02 1312743 /usr/lib64/libz.so.1.2.3 3e44a14000-3e44c13000 ---p 00014000 08:02 1312743 /usr/lib64/libz.so.1.2.3 3e44c13000-3e44c14000 rw-p 00013000 08:02 1312743 /usr/lib64/libz.so.1.2.3 3e44e00000-3e44e0d000 r-xp 00000000 08:02 14291931 /lib64/libgcc_s-4.1.2-20070626.so.1 3e44e0d000-3e4500d000 ---p 0000d000 08:02 14291931 /lib64/libgcc_s-4.1.2-20070626.so.1 3e4500d000-3e4500e000 rw-p 0000d000 08:02 14291931 /lib64/libgcc_s-4.1.2-20070626.so.1 3e45200000-3e45205000 r-xp 00000000 08:02 14291934 /lib64/libcrypt-2.5.so 3e45205000-3e45404000 ---p 00005000 08:02 14291934 /lib64/libcrypt-2.5.so 3e45404000-3e45405000 r--p 00004000 08:02 14291934 /lib64/libcrypt-2.5.so 3e45405000-3e45406000 rw-p 00005000 08:02 14291934 /lib64/libcrypt-2.5.so 3e45406000-3e45434000 rw-p 3e45406000 00:00 0 3e45600000-3e456e6000 r-xp 00000000 08:02 1312308 /usr/lib64/libstdc++.so.6.0.8 3e456e6000-3e458e5000 ---p 000e6000 08:02 1312308 /usr/lib64/libstdc++.so.6.0.8 3e458e5000-3e458eb000 r--p 000e5000 08:02 1312308 /usr/lib64/libstdc++.so.6.0.8 3e458eb000-3e458ee000 rw-p 000eb000 08:02 1312308 /usr/lib64/libstdc++.so.6.0.8 3e458ee000-3e45900000 rw-p 3e458ee000 00:00 0 2aaaaaaab000-2aaaaaaae000 rw-p 2aaaaaaab000 00:00 0 2aaaaaabe000-2aaaaaac3000 rw-p 2aaaaaabe000 00:00 0 2aaaaaac3000-2aaaaaacd000 r-xp 00000000 08:02 14291676 /lib64/libnss_files-2.5.so 2aaaaaacd000-2aaaaaccc000 ---p 0000a000 08:02 14291676 /lib64/libnss_files-2.5.so 2aaaaaccc000-2aaaaaccd000 r--p 00009000 08:02 14291676 /lib64/libnss_files-2.5.so 2aaaaaccd000-2aaaaacce000 rw-p 0000a000 08:02 14291676 /lib64/libnss_files-2.5.so 2aaaaacce000-2aaabdc24000 rw-p 2aaaaacce000 00:00 0 2aaac0000000-2aaac0021000 rw-p 2aaac0000000 00:00 0 2aaac0021000-2aaac4000000 ---p 2aaac0021000 00:00 0 7fffbe9a9000-7fffbe9c0000 rw-p 7fffbe9a9000 00:00 0 [stack] ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso] Projecting RH Surfs Computing relative cost