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

########################################################

#--------------------------------------------
#@# 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