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