Hi all,

Congrats on the new version! I've been excited to see how the use of data from T2 images could help pial surface estimation, but I'm encountering a problem with getting that to work. It seems to be failing to properly execute the bbregister command built into this part of the new recon-all script.

My command was 'recon-all -s <subjid> -i <path/to/T1dcm> -T2 <path/to/T2dcm> -all -T2pial', from an x86_64 Linux platform, and using the stable release of FreeSurfer 5.2. Appended below my signature is the full log of errors that I get (which I've replicated with another subject). Any advice or insights would be much appreciated.

Thanks!

Warren

-- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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#-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Wed Mar 6 02:52:25 EST 2013

bbregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --lta /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta --init-fsl --T2

Log file is /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat.log Wed Mar 6 02:52:25 EST 2013

setenv SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer cd /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/bin/bbregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --lta /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz... TR=2800.00, TE=327.00, TI=-1.00, flip angle=120.00 i_ras = (0.0328993, -0.992771, -0.115425) j_ras = (0.0303427, 0.116427, -0.992736) k_ras = (-0.998998, -0.029158, -0.0339537) writing to /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii... fslregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister --dof 6 --fsvol brainmask

Log file is /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fslregister.log

Wed Mar 6 02:52:25 EST 2013 --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ rc-twice Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts mri_convert ERROR: could not determine file for /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/ERROR: /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/ERROR: /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii

mri_convert: extra arguments ("not" and following)

type mri_convert -u for usage

-------------------------------------- /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii --frame 0 mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/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 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii... TR=2800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0328993, -0.992771, -0.115425) j_ras = (0.0303427, 0.116427, -0.992736) k_ras = (-0.998998, -0.029158, -0.0339537) keeping frame 0 writing to /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii... Mov determinant is -1.72201 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts tkregister2_cmdl --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/reg0.15619.dat --regheader --fslregout /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat0 --s 2012_T2 --noedit tkregister_tcl /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii reg file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/reg0.15619.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 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/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 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.198 0.000 0.000 115.000; 0.000 0.000 1.200 -86.400; 0.000 -1.198 0.000 115.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.033 0.993 0.115 0.704; -0.999 -0.029 -0.034 -0.506; -0.030 -0.116 0.993 1.573; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.033 0.993 0.115 0.704; -0.999 -0.029 -0.034 -0.506; -0.030 -0.116 0.993 1.573; 0.000 0.000 0.000 1.000; Determinant 1 subject = 2012_T2 RegMat --------------------------- -0.033 0.993 0.115 0.704; -0.999 -0.029 -0.034 -0.506; -0.030 -0.116 0.993 1.573; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1.72201, ref det = -1 Wed Mar 6 02:52:29 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts flirt.fsl -ref /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii -in /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/fslmat0.trans.mat -schedule /chb/pices/arch/x86_64-Linux/packages/fsl419/etc/flirtsch/xyztrans.sch -init /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister ERROR: Could not open image /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Mar 6 02:52:29 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts flirt.fsl -ref /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii -in /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat -init /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/fslmat0.trans.mat -schedule /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister ERROR: Could not open image /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) tkregister2_cmdl --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --fslreg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat --noedit tkregister_tcl /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/tktools/tkregister2.tcl ERROR: cannot open /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat cat: /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat: No such file or directory tmp: Subscript out of range.

Started at Wed Mar 6 02:52:25 EST 2013 Ended at Wed Mar 6 02:52:29 EST 2013

fslregister Done

To check results, run: tkregister2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --surf orig

mri_segreg --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --init-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --out-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/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 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat mri_segreg --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --init-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/bbr.pass1.dat --out-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat.param --surf white --cur-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/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 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/bbr.pass1.dat tkregister2_cmdl --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat --noedit --ltaout /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta regio_read_register(): No such file or directory Could not open /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat tkregister_tcl /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz reg file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ERROR: reading /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat Cleaning up

Started at Wed Mar 6 02:52:25 EST 2013 Ended at Wed Mar 6 02:52:29 EST 2013 BBR-Run-Time-Sec 4

bbregister Done To check results, run: tkregister2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat --surf

mri_convert -at /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta -rl /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/T2.mgz

mri_convert -at /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta -rl /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/T2.mgz ltaReadFile(/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta): can't open file $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz... TR=2800.00, TE=327.00, TI=-1.00, flip angle=120.00 i_ras = (0.0328993, -0.992771, -0.115425) j_ras = (0.0303427, 0.116427, -0.992736) k_ras = (-0.998998, -0.029158, -0.0339537) INFO: Reading transformation from file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 2012_T2 exited with ERRORS at Wed Mar 6 02:52:30 EST 2013