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
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
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
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Dear all,
Here is the output of the mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii.The image that I'm using as a T2 is, in fact, the b0 from the DTI. It's is the highest resolution volume I have, so I don't have many alternatives.
Volume information for b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii type: nii dimensions: 160 x 160 x 80 voxel sizes: 1.6000, 1.6000, 2.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 10800.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.9968, y_r = 0.0651, z_r = -0.0464, c_r = 0.3105 : x_a = 0.0726, y_a = 0.9806, z_a = -0.1824, c_a = 24.5431 : x_s = -0.0336, y_s = 0.1851, z_s = 0.9821, c_s = -17.0332 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -1.5949 0.1042 -0.0928 123.2741 0.1161 1.5689 -0.3647 -95.6693 -0.0538 0.2962 1.9643 -114.9972 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -5.12001
ras to voxel transform: -0.6230 0.0454 -0.0210 78.7222 0.0407 0.6128 0.1157 66.9172 -0.0232 -0.0912 0.4911 50.6094 0.0000 0.0000 0.0000 1.0000
I also attach the "normal" streamline log file and the "pial-refinement" log file.
Thanks in advance!
Eduard
________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Charles Malpas [c.malpas@student.unimelb.edu.au] Enviat el: dijous, 18 / abril / 2013 02:11 Per a: Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.aumailto:c.malpas@student.unimelb.edu.au Skype: charles.malpas
Dear FS experts,
Any idea about that problem? Does anybody has used this pial correction technique?
Thanks in advance
Best regards,
Eduard ________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Eduard Vilaplana Martinez [EVilaplana@santpau.cat] Enviat el: dijous, 18 / abril / 2013 11:05 Per a: Charles Malpas; Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
Dear all,
Here is the output of the mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii.The image that I'm using as a T2 is, in fact, the b0 from the DTI. It's is the highest resolution volume I have, so I don't have many alternatives.
Volume information for b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii type: nii dimensions: 160 x 160 x 80 voxel sizes: 1.6000, 1.6000, 2.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 10800.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.9968, y_r = 0.0651, z_r = -0.0464, c_r = 0.3105 : x_a = 0.0726, y_a = 0.9806, z_a = -0.1824, c_a = 24.5431 : x_s = -0.0336, y_s = 0.1851, z_s = 0.9821, c_s = -17.0332 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -1.5949 0.1042 -0.0928 123.2741 0.1161 1.5689 -0.3647 -95.6693 -0.0538 0.2962 1.9643 -114.9972 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -5.12001
ras to voxel transform: -0.6230 0.0454 -0.0210 78.7222 0.0407 0.6128 0.1157 66.9172 -0.0232 -0.0912 0.4911 50.6094 0.0000 0.0000 0.0000 1.0000
I also attach the "normal" streamline log file and the "pial-refinement" log file.
Thanks in advance!
Eduard
________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Charles Malpas [c.malpas@student.unimelb.edu.au] Enviat el: dijous, 18 / abril / 2013 02:11 Per a: Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.aumailto:c.malpas@student.unimelb.edu.au Skype: charles.malpas
Hi all,
I also had this same problem with -T2pial, posted on the archives back in March. I, too, have a log where mri_convert is given an input of "ERROR: could not determine file for ...", and I believe I've traced it back to this early line in bbregister (our copy is dated at 2/23/2013, revision 1.49.2.2): "set fsvol = brainmask". In our recon-all script (dated 2/19/2013, revision 1.379.2.65), the T2pial code block runs this command:
bbregister --s $subjid --mov $t2flairraw --lta $mdir/transforms/${t2flair}raw.lta --init-fsl --T2
With init-fsl set to true, bbregister then runs an fslregister command containing "--fslvol $fsvol", which ends up being interpreted as --fsvol $mdir/brainmask and generating an error. When I manually ran the same bbregister command with --fsvol brainmask.mgz added, mri_convert got the correct input and everything worked.
Is it possible that our versions of recon-all and/or bbregister are not the most up-to-date copies?
Warren
On Apr 22, 2013, at 7:56 AM, Eduard Vilaplana Martinez wrote:
Dear FS experts,
Any idea about that problem? Does anybody has used this pial correction technique?
Thanks in advance
Best regards,
Eduard ________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Eduard Vilaplana Martinez [EVilaplana@santpau.cat] Enviat el: dijous, 18 / abril / 2013 11:05 Per a: Charles Malpas; Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
Dear all,
Here is the output of the mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii.The image that I'm using as a T2 is, in fact, the b0 from the DTI. It's is the highest resolution volume I have, so I don't have many alternatives.
Volume information for b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii type: nii dimensions: 160 x 160 x 80 voxel sizes: 1.6000, 1.6000, 2.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 10800.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.9968, y_r = 0.0651, z_r = -0.0464, c_r = 0.3105 : x_a = 0.0726, y_a = 0.9806, z_a = -0.1824, c_a = 24.5431 : x_s = -0.0336, y_s = 0.1851, z_s = 0.9821, c_s = -17.0332 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -1.5949 0.1042 -0.0928 123.2741 0.1161 1.5689 -0.3647 -95.6693 -0.0538 0.2962 1.9643 -114.9972 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -5.12001
ras to voxel transform: -0.6230 0.0454 -0.0210 78.7222 0.0407 0.6128 0.1157 66.9172 -0.0232 -0.0912 0.4911 50.6094 0.0000 0.0000 0.0000 1.0000
I also attach the "normal" streamline log file and the "pial-refinement" log file.
Thanks in advance!
Eduard
De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Charles Malpas [c.malpas@student.unimelb.edu.au] Enviat el: dijous, 18 / abril / 2013 02:11 Per a: Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
-- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.aumailto:c.malpas@student.unimelb.edu.au Skype: charles.malpas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
This is a problem that originated with newer versions of tcsh. Try using the version of bbregister from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 04/22/2013 02:28 PM, Winter, Warren wrote:
Hi all,
I also had this same problem with -T2pial, posted on the archives back in March. I, too, have a log where mri_convert is given an input of "ERROR: could not determine file for ...", and I believe I've traced it back to this early line in bbregister (our copy is dated at 2/23/2013, revision 1.49.2.2): "set fsvol = brainmask". In our recon-all script (dated 2/19/2013, revision 1.379.2.65), the T2pial code block runs this command:
bbregister --s $subjid --mov $t2flairraw --lta $mdir/transforms/${t2flair}raw.lta --init-fsl --T2
With init-fsl set to true, bbregister then runs an fslregister command containing "--fslvol $fsvol", which ends up being interpreted as --fsvol $mdir/brainmask and generating an error. When I manually ran the same bbregister command with --fsvol brainmask.mgz added, mri_convert got the correct input and everything worked.
Is it possible that our versions of recon-all and/or bbregister are not the most up-to-date copies?
Warren
On Apr 22, 2013, at 7:56 AM, Eduard Vilaplana Martinez wrote:
Dear FS experts,
Any idea about that problem? Does anybody has used this pial correction technique?
Thanks in advance
Best regards,
Eduard ________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Eduard Vilaplana Martinez [EVilaplana@santpau.cat] Enviat el: dijous, 18 / abril / 2013 11:05 Per a: Charles Malpas; Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
Dear all,
Here is the output of the mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii.The image that I'm using as a T2 is, in fact, the b0 from the DTI. It's is the highest resolution volume I have, so I don't have many alternatives.
Volume information for b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii type: nii dimensions: 160 x 160 x 80 voxel sizes: 1.6000, 1.6000, 2.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 10800.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.9968, y_r = 0.0651, z_r = -0.0464, c_r = 0.3105 : x_a = 0.0726, y_a = 0.9806, z_a = -0.1824, c_a = 24.5431 : x_s = -0.0336, y_s = 0.1851, z_s = 0.9821, c_s = -17.0332 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -1.5949 0.1042 -0.0928 123.2741 0.1161 1.5689 -0.3647 -95.6693 -0.0538 0.2962 1.9643 -114.9972 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -5.12001
ras to voxel transform: -0.6230 0.0454 -0.0210 78.7222 0.0407 0.6128 0.1157 66.9172 -0.0232 -0.0912 0.4911 50.6094 0.0000 0.0000 0.0000 1.0000
I also attach the "normal" streamline log file and the "pial-refinement" log file.
Thanks in advance!
Eduard
De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Charles Malpas [c.malpas@student.unimelb.edu.au] Enviat el: dijous, 18 / abril / 2013 02:11 Per a: Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.aumailto:c.malpas@student.unimelb.edu.au Skype: charles.malpas
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Thank you for that -- the problem is indeed solved with this newer version of bbregister.
On Apr 22, 2013, at 2:45 PM, Douglas N Greve wrote:
This is a problem that originated with newer versions of tcsh. Try using the version of bbregister from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 04/22/2013 02:28 PM, Winter, Warren wrote: Hi all,
I also had this same problem with -T2pial, posted on the archives back in March. I, too, have a log where mri_convert is given an input of "ERROR: could not determine file for ...", and I believe I've traced it back to this early line in bbregister (our copy is dated at 2/23/2013, revision 1.49.2.2): "set fsvol = brainmask". In our recon-all script (dated 2/19/2013, revision 1.379.2.65), the T2pial code block runs this command:
bbregister --s $subjid --mov $t2flairraw --lta $mdir/transforms/${t2flair}raw.lta --init-fsl --T2
With init-fsl set to true, bbregister then runs an fslregister command containing "--fslvol $fsvol", which ends up being interpreted as --fsvol $mdir/brainmask and generating an error. When I manually ran the same bbregister command with --fsvol brainmask.mgz added, mri_convert got the correct input and everything worked.
Is it possible that our versions of recon-all and/or bbregister are not the most up-to-date copies?
Warren
On Apr 22, 2013, at 7:56 AM, Eduard Vilaplana Martinez wrote:
Dear FS experts,
Any idea about that problem? Does anybody has used this pial correction technique?
Thanks in advance
Best regards,
Eduard ________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Eduard Vilaplana Martinez [EVilaplana@santpau.cat] Enviat el: dijous, 18 / abril / 2013 11:05 Per a: Charles Malpas; Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
Dear all,
Here is the output of the mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii.The image that I'm using as a T2 is, in fact, the b0 from the DTI. It's is the highest resolution volume I have, so I don't have many alternatives.
Volume information for b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii type: nii dimensions: 160 x 160 x 80 voxel sizes: 1.6000, 1.6000, 2.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 10800.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.9968, y_r = 0.0651, z_r = -0.0464, c_r = 0.3105 : x_a = 0.0726, y_a = 0.9806, z_a = -0.1824, c_a = 24.5431 : x_s = -0.0336, y_s = 0.1851, z_s = 0.9821, c_s = -17.0332 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -1.5949 0.1042 -0.0928 123.2741 0.1161 1.5689 -0.3647 -95.6693 -0.0538 0.2962 1.9643 -114.9972 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -5.12001
ras to voxel transform: -0.6230 0.0454 -0.0210 78.7222 0.0407 0.6128 0.1157 66.9172 -0.0232 -0.0912 0.4911 50.6094 0.0000 0.0000 0.0000 1.0000
I also attach the "normal" streamline log file and the "pial-refinement" log file.
Thanks in advance!
Eduard
________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Charles Malpas [c.malpas@student.unimelb.edu.au] Enviat el: dijous, 18 / abril / 2013 02:11 Per a: Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
-- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.aumailto:c.malpas@student.unimelb.edu.au Skype: charles.malpas
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-- 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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
Thanks Warren for finding and fixing this, and testing!
Eduardo, can you give this version of bbregister (link below) a try? Copy it to your $FREESURFER_HOME/bin directory. You may also need to run: chmod a+x $FREESURFER_HOME/bin/bbregister
Nick
On Mon, 2013-04-22 at 19:00 +0000, Winter, Warren wrote:
Thank you for that -- the problem is indeed solved with this newer version of bbregister.
On Apr 22, 2013, at 2:45 PM, Douglas N Greve wrote:
This is a problem that originated with newer versions of tcsh. Try using the version of bbregister from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 04/22/2013 02:28 PM, Winter, Warren wrote:
Hi all,
I also had this same problem with -T2pial, posted on the archives back in March. I, too, have a log where mri_convert is given an input of "ERROR: could not determine file for ...", and I believe I've traced it back to this early line in bbregister (our copy is dated at 2/23/2013, revision 1.49.2.2): "set fsvol = brainmask". In our recon-all script (dated 2/19/2013, revision 1.379.2.65), the T2pial code block runs this command:
bbregister --s $subjid --mov $t2flairraw --lta $mdir/transforms/${t2flair}raw.lta --init-fsl --T2
With init-fsl set to true, bbregister then runs an fslregister command containing "--fslvol $fsvol", which ends up being interpreted as --fsvol $mdir/brainmask and generating an error. When I manually ran the same bbregister command with --fsvol brainmask.mgz added, mri_convert got the correct input and everything worked.
Is it possible that our versions of recon-all and/or bbregister are not the most up-to-date copies?
Warren
On Apr 22, 2013, at 7:56 AM, Eduard Vilaplana Martinez wrote:
Dear FS experts,
Any idea about that problem? Does anybody has used this pial correction technique?
Thanks in advance
Best regards,
Eduard ________________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Eduard Vilaplana Martinez [EVilaplana@santpau.cat] Enviat el: dijous, 18 / abril / 2013 11:05 Per a: Charles Malpas; Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
Dear all,
Here is the output of the mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii.The image that I'm using as a T2 is, in fact, the b0 from the DTI. It's is the highest resolution volume I have, so I don't have many alternatives.
Volume information for b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii type: nii dimensions: 160 x 160 x 80 voxel sizes: 1.6000, 1.6000, 2.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 10800.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.9968, y_r = 0.0651, z_r = -0.0464, c_r = 0.3105 : x_a = 0.0726, y_a = 0.9806, z_a = -0.1824, c_a = 24.5431 : x_s = -0.0336, y_s = 0.1851, z_s = 0.9821, c_s = -17.0332 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -1.5949 0.1042 -0.0928 123.2741 0.1161 1.5689 -0.3647 -95.6693 -0.0538 0.2962 1.9643 -114.9972 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -5.12001
ras to voxel transform: -0.6230 0.0454 -0.0210 78.7222 0.0407 0.6128 0.1157 66.9172 -0.0232 -0.0912 0.4911 50.6094 0.0000 0.0000 0.0000 1.0000
I also attach the "normal" streamline log file and the "pial-refinement" log file.
Thanks in advance!
Eduard
De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Charles Malpas [c.malpas@student.unimelb.edu.au] Enviat el: dijous, 18 / abril / 2013 02:11 Per a: Freesurfer@nmr.mgh.harvard.edu Tema: Re: [Freesurfer] T2 pial
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.aumailto:c.malpas@student.unimelb.edu.au Skype: charles.malpas
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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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-
Charles Malpas -
Douglas N Greve -
Eduard Vilaplana Martinez -
Nick Schmansky -
Winter, Warren