Dear FreeSurfer experts,
First of all, congrats for this new 5.2 stable version.
My name is Eduard, and I'm trying to perform de T2 pial refinement in a
pre-processed subject with the B0 image from a DTI. I used that command:
recon-all -autorecon3 -T2pial -s ACC019/ -T2
/home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii
Being "ACC019" the subject ID and
"/home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii"
the path to the T2 nifti.
Whatever I do, it always return me the following error. Any suggestions would
be greatly appreciated. Thanks in advance.
@# Refine Pial Surfs w/ T2/FLAIR Wed Apr 17 14:37:42 CEST 2013
bbregister --s ACC019 --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl
--T2
Log file is
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.log
Wed Apr 17 14:37:42 CEST 2013
setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2
cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
/usr/local/freesurfer/bin/bbregister --s ACC019 --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl
--T2
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25
21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996796, 0.0725774, -0.0336276)
j_ras = (0.065149, 0.980551, 0.185135)
k_ras = (-0.0464102, -0.182351, 0.982138)
writing to
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
fslregister --s ACC019 --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
--reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
--niters 1 --maxangle 90 --nobetmov --tmp
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister
--dof 6 --fsvol brainmask
Log file is
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fslregister.log
Wed Apr 17 14:37:42 CEST 2013
--s ACC019 --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
--reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
--niters 1 --maxangle 90 --nobetmov --tmp
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister
--dof 6 --fsvol brainmask
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
linux-To-be-filled-by-O-E-M
Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25
21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
mri_convert ERROR: could not determine file for
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR:
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
mri_convert ERROR: could not determine file for
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR:
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
--------------------------------------
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
mri_convert
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
--frame 0
mri_convert
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/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
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996796, 0.0725774, -0.0336276)
j_ras = (0.065149, 0.980551, 0.185135)
k_ras = (-0.0464102, -0.182351, 0.982138)
keeping frame 0
writing to
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii...
Mov determinant is -5.12001
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
tkregister2_cmdl --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
--reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat
--regheader --fslregout
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0
--s ACC019 --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
reg file
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.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 /home/linux/Escritorio/COHORTE_T2/ACC019/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
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.600 0.000 0.000 128.000;
0.000 0.000 2.000 -80.000;
0.000 -1.600 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) --------
0.997 -0.073 0.034 0.214;
-0.046 -0.182 0.982 -30.911;
-0.065 -0.981 -0.185 1.512;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
0.997 -0.073 0.034 0.214;
-0.046 -0.182 0.982 -30.911;
-0.065 -0.981 -0.185 1.512;
0.000 0.000 0.000 1.000;
Determinant 1
subject = ACC019
RegMat ---------------------------
0.997 -0.073 0.034 0.214;
-0.046 -0.182 0.982 -30.911;
-0.065 -0.981 -0.185 1.512;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -5.12001, ref det = -1
Wed Apr 17 14:37:44 CEST 2013
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
flirt.fsl -ref
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
-in
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
-90 90 -verbose 0 -omat
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat
-schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0
** ERROR (nifti_image_read): failed to find header file for
'/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
** ERROR:
nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister):
bad header info
ERROR: failed to open file
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
ERROR: Could not open image
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
Image Exception : #22 :: Failed to read volume
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped)
Wed Apr 17 14:37:44 CEST 2013
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
flirt.fsl -ref
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
-in
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
-90 90 -verbose 0 -omat
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
-init
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat
-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
** ERROR (nifti_image_read): failed to find header file for
'/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
** ERROR:
nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister):
bad header info
ERROR: failed to open file
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
ERROR: Could not open image
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
Image Exception : #22 :: Failed to read volume
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped)
tkregister2_cmdl --s ACC019 --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
--reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
--fslreg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
--noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
ERROR: cannot open
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
cat:
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat:
No such file or directory
tmp: Subscript out of range.
Started at Wed Apr 17 14:37:42 CEST 2013
Ended at Wed Apr 17 14:37:44 CEST 2013
fslregister Done
To check results, run:
tkregister2 --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
--reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
--surf orig
mri_segreg --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
--init-reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
--out-reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/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
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
mri_segreg --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
--init-reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
--out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/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
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.mincost --dof
6 --nmax 36 --param
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.param --surf
white --cur-reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/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
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
tkregister2_cmdl --mov
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --noedit
--ltaout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
regio_read_register(): No such file or directory
Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
reg file /home/linux/Escritorio/COHORTE_T2/ACC019/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 /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
Cleaning up
Started at Wed Apr 17 14:37:42 CEST 2013
Ended at Wed Apr 17 14:37:45 CEST 2013
BBR-Run-Time-Sec 3
bbregister Done
To check results, run:
tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
--reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --surf
mri_convert -at
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz
mri_convert -at
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz
ltaReadFile(/home/linux/Escritorio/COHORTE_T2/ACC019/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 /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996796, 0.0725774, -0.0336276)
j_ras = (0.065149, 0.980551, 0.185135)
k_ras = (-0.0464102, -0.182351, 0.982138)
INFO: Reading transformation from file
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
No such file or directory
ERROR: Reading transform from file
/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25
21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ACC019 exited with ERRORS at Wed Apr 17 14:37:45 CEST 2013
For more details, see the log file
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
