Logfile for bbregister Mon Aug 24 17:09:39 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_1045_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --dti --init-fsl --reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/CVRAM_1045_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_1045_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii mri_convert /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_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, -4.65661e-09, -9.31323e-10) j_ras = (6.0536e-09, 1, 2.98023e-08) k_ras = (-1.86265e-09, 0, 1) writing to /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii... fslregister --s CVRAM_1045_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister --dof 6 Log file is /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fslregister.log Mon Aug 24 17:09:40 EDT 2009 --s CVRAM_1045_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_recon/mri/brainmask.mgz /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/refvol.fslregister.nii mri_convert /autofs/space/lang_012/users/CVRAM/CVRAM_1045_recon/mri/brainmask.mgz /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_recon/mri/brainmask.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.5775e-09, 5.01362e-10) j_ras = (-7.17543e-11, -2.72532e-09, -1) k_ras = (2.14413e-09, 1, -2.47023e-08) writing to /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/space/orion_002/users/DTI/SCRIPTS mri_convert /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii --frame 0 mri_convert /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_dti/tmp.bbregister.27403/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.65661e-09, -9.31323e-10) j_ras = (6.0536e-09, 1, 2.98023e-08) k_ras = (-1.86265e-09, 0, 1) keeping frame 0 writing to /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii... /autofs/space/orion_002/users/DTI/SCRIPTS tkregister2_cmdl --mov /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/reg0.27445.dat --regheader --fslregout /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fsl.mat0 --s CVRAM_1045_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_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii reg file /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/reg0.27445.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_1045_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_1045_dti/tmp.bbregister.27403/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 -0.011; -0.000 -0.000 1.000 -22.143; 0.000 -1.000 -0.000 -13.995; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 0.000 -0.011; -0.000 -0.000 1.000 -22.143; 0.000 -1.000 -0.000 -13.995; 0.000 0.000 0.000 1.000; Determinant 1 subject = CVRAM_1045_recon RegMat --------------------------- 1.000 -0.000 0.000 -0.011; -0.000 -0.000 1.000 -22.143; 0.000 -1.000 -0.000 -13.995; 0.000 0.000 0.000 1.000; register: file /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/reg0.27445.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 Mon Aug 24 17:09:44 EDT 2009 /autofs/space/orion_002/users/DTI/SCRIPTS flirt -ref /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/refvol.fslregister.nii -in /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii -bins 256 -omat /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_dti/tmp.bbregister.27403/reg.init.dat.fsl.mat0 tkregister2_cmdl --s CVRAM_1045_recon --mov /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat --fslreg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/dev/lib/tcl/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.004 -0.003 -0.108; -0.003 -0.001 -1.000 169.355; 0.004 1.000 -0.001 -13.748; 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_1045_dti/tmp.bbregister.27403/template.nii reg file /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_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_1045_dti/tmp.bbregister.27403/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 -0.004 -0.003 -0.775; 0.003 -0.001 1.000 -19.179; -0.004 -1.000 -0.001 -13.297; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.004 -0.003 -0.775; 0.003 -0.001 1.000 -19.179; -0.004 -1.000 -0.001 -13.297; 0.000 0.000 0.000 1.000; Determinant 1 subject = CVRAM_1045_recon RegMat --------------------------- 1.000 -0.004 -0.003 -0.775; 0.003 -0.001 1.000 -19.179; -0.004 -1.000 -0.001 -13.297; 0.000 0.000 0.000 1.000; register: file /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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 17:09:40 EDT 2009 Ended at Mon Aug 24 17:10:11 EDT 2009 fslregister Done To check results, run: tkregister2 --mov /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii --reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat --surf orig mri_segreg --mov /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii --init-reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat --out-reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_dti/tmp.bbregister.27403/template.nii --init-reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat --out-reg /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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_1045_dti/tmp.bbregister.27403/template.nii regfile /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat subject CVRAM_1045_recon dof 6 outregfile /autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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 1252146426 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 -0.003 -0.775; 0.003 -0.001 1.000 -19.179; -0.004 -1.000 -0.001 -13.297; 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