Log file is /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.dat.log Mon Mar 11 14:01:11 EST 2013 setenv SUBJECTS_DIR /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2 cd /bilhome/cmalpas/selenate/MRI/freesurfer/input5.2 /usr/local/freesurfer5.2/bin/bbregister --s 112-M101 --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz --lta /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.lta --init-fsl --T2 --debug $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux bee1 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer5.2 mri_convert /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii mri_convert /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz... TR=5000.00, TE=355.00, TI=1800.00, flip angle=120.00 i_ras = (0.0226994, -0.999742, -3.04243e-08) j_ras = (-0.0112768, -0.000256012, -0.999936) k_ras = (-0.999679, -0.022698, 0.0112797) writing to /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii... fslregister --s 112-M101 --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii --reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister --dof 6 --fsvol brainmask Log file is /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat.fslregister.log Mon Mar 11 14:01:17 EST 2013 --s 112-M101 --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii --reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ bee1 Linux bee1 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /bilhome/cmalpas/selenate/MRI/freesurfer/input5.2 mri_convert ERROR: could not determine file for /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/ERROR: /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/ERROR: /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /bilhome/cmalpas/selenate/MRI/freesurfer/input5.2 mri_convert /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/movvol.fslregister.nii --frame 0 mri_convert /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/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 /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0226994, -0.999742, -3.04243e-08) j_ras = (-0.0112768, -0.000256012, -0.999936) k_ras = (-0.999679, -0.022698, 0.0112797) keeping frame 0 writing to /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/movvol.fslregister.nii... Mov determinant is -0.25 /bilhome/cmalpas/selenate/MRI/freesurfer/input5.2 tkregister2_cmdl --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/movvol.fslregister.nii --reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/reg0.65033.dat --regheader --fslregout /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat.fsl.mat0 --s 112-M101 --noedit tkregister_tcl /usr/local/freesurfer5.2/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/movvol.fslregister.nii reg file /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/reg0.65033.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 /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/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 /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.500 0.000 0.000 128.000; 0.000 0.000 1.000 -80.000; 0.000 -0.500 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) -------- -0.023 1.000 0.000 -0.000; -1.000 -0.023 0.011 0.000; 0.011 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.023 1.000 0.000 -0.000; -1.000 -0.023 0.011 0.000; 0.011 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = 112-M101 RegMat --------------------------- -0.023 1.000 0.000 -0.000; -1.000 -0.023 0.011 0.000; 0.011 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.25, ref det = -1 Mon Mar 11 14:01:26 EST 2013 /bilhome/cmalpas/selenate/MRI/freesurfer/input5.2 flirt.fsl -ref /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister.nii -in /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for '/bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister ERROR: Could not open image /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Mon Mar 11 14:01:27 EST 2013 /bilhome/cmalpas/selenate/MRI/freesurfer/input5.2 flirt.fsl -ref /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister.nii -in /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat.fsl.mat -init /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer5.2/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for '/bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister ERROR: Could not open image /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) tkregister2_cmdl --s 112-M101 --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii --reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat --fslreg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer5.2/tktools/tkregister2.tcl ERROR: cannot open /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat.fsl.mat cat: /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Mon Mar 11 14:01:17 EST 2013 Ended at Mon Mar 11 14:01:27 EST 2013 fslregister Done To check results, run: tkregister2 --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii --reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat --surf orig mri_segreg --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii --init-reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat --out-reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/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 regio_read_register(): No such file or directory Could not open /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.init.dat mri_segreg --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/template.nii --init-reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/bbr.pass1.dat --out-reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/tmp.bbregister.64997/bbr.pass1.dat tkregister2_cmdl --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz --reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.dat --noedit --ltaout /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.lta tkregister_tcl /usr/local/freesurfer5.2/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz reg file /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.023 1.000 -0.001 0.126; -1.000 -0.023 0.018 -0.076; 0.018 0.002 1.000 0.161; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/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 /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz Tmov: -------------------- -0.500 0.000 0.000 128.000; 0.000 0.000 1.000 -80.000; 0.000 -0.500 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.023 1.000 -0.001 0.126; -1.000 -0.023 0.018 -0.076; 0.018 0.002 1.000 0.161; 0.000 0.000 0.000 1.000; Determinant 1 subject = 112-M101 RegMat --------------------------- -0.023 1.000 -0.001 0.126; -1.000 -0.023 0.018 -0.076; 0.018 0.002 1.000 0.161; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.001 0.006 -0.020; 0.001 1.000 0.001 -0.119; -0.006 -0.001 1.000 -0.142; 0.000 0.000 0.000 1.000; transformed matrix: -0.012 0.009 1.000 48.877; -0.001 0.500 -0.018 1.729; -0.500 -0.001 -0.023 257.914; 0.000 0.000 0.000 1.000; Cleaning up Started at Mon Mar 11 14:01:11 EST 2013 Ended at Mon Mar 11 14:01:46 EST 2013 BBR-Run-Time-Sec 35 bbregister Done To check results, run: tkregister2 --mov /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/orig/FLAIRraw.mgz --reg /bilhome/cmalpas/selenate/MRI/freesurfer/subjects5.2/112-M101/mri/transforms/FLAIRraw.dat --surf