Hi All,
I have a similar error, which I traced back (I think!) to bbregister failing to write FLAIRraw.lta. My only solution was to download the subject directories from our linux (RedHat) cluster and run the registration on an OSX binary. This then creates the .lta file and I upload it back to the linux cluster to run -FLAIRpial which creates the FLAIR.mgz volume. Weird, I know!
Kind regards,
- Charles
On 18 April 2013 03:15, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Eduard,
Can you send the whole recon-all.log file? The error show below is a strange one. It appears as if the string "ERROR: could not determine file" is the input to mri_convert, and I'm not sure how that can happen.
Also double check (by viewing in freeview) that T2raw.mgz is a valid file (ie, looks like a T2-space brain).
and perhaps send output of:
mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii
Nick
On Wed, 2013-04-17 at 13:04 +0000, Eduard Vilaplana Martinez wrote:
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
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