Eduard,
Can you send the whole recon-all.log file? The error show below is a
strange one. It appears as if the string "ERROR: could not determine
file" is the input to mri_convert, and I'm not sure how that can happen.
Also double check (by viewing in freeview) that T2raw.mgz is a valid
file (ie, looks like a T2-space brain).
and perhaps send output of:
mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii
Nick
On Wed, 2013-04-17 at 13:04 +0000, Eduard Vilaplana Martinez wrote:
> Dear FreeSurfer experts,
>
> First of all, congrats for this new 5.2 stable version.
>
> My name is Eduard, and I'm trying to perform de T2 pial refinement in a
> pre-processed subject with the B0 image from a DTI. I used that command:
>
>
> recon-all -autorecon3 -T2pial -s ACC019/ -T2
> /home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii
>
> Being "ACC019" the subject ID and
> "/home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii"
> the path to the T2 nifti.
>
> Whatever I do, it always return me the following error. Any suggestions would
> be greatly appreciated. Thanks in advance.
>
>
> @# Refine Pial Surfs w/ T2/FLAIR Wed Apr 17 14:37:42 CEST 2013
>
> bbregister --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl
> --T2
>
> Log file is
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.log
> Wed Apr 17 14:37:42 CEST 2013
>
> setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2
> cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> /usr/local/freesurfer/bin/bbregister --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl
> --T2
>
> $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
> Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25
> 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> FREESURFER_HOME /usr/local/freesurfer
> mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
> TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.996796, 0.0725774, -0.0336276)
> j_ras = (0.065149, 0.980551, 0.185135)
> k_ras = (-0.0464102, -0.182351, 0.982138)
> writing to
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
> fslregister --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --niters 1 --maxangle 90 --nobetmov --tmp
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister
> --dof 6 --fsvol brainmask
>
> Log file is
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fslregister.log
>
> Wed Apr 17 14:37:42 CEST 2013
> --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --niters 1 --maxangle 90 --nobetmov --tmp
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister
> --dof 6 --fsvol brainmask
> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
> linux-To-be-filled-by-O-E-M
> Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25
> 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> nIters 1
> --------------------------------------
> /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> mri_convert ERROR: could not determine file for
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR:
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> mri_convert ERROR: could not determine file for
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR:
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
>
>
> mri_convert: extra arguments ("not" and following)
>
> type mri_convert -u for usage
>
> --------------------------------------
> /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> mri_convert
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
>
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> --frame 0
> mri_convert
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
>
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> --frame 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
> TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.996796, 0.0725774, -0.0336276)
> j_ras = (0.065149, 0.980551, 0.185135)
> k_ras = (-0.0464102, -0.182351, 0.982138)
> keeping frame 0
> writing to
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii...
> Mov determinant is -5.12001
> /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> tkregister2_cmdl --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat
> --regheader --fslregout
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0
> --s ACC019 --noedit
> tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
> INFO: no target volume specified, assuming FreeSurfer orig volume.
> target volume orig
> movable volume
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> reg file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat
> LoadVol 0
> ZeroCRAS 0
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
> INFO: loading target /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
> Ttarg: --------------------
> -1.000 0.000 0.000 128.000;
> 0.000 0.000 1.000 -128.000;
> 0.000 -1.000 0.000 128.000;
> 0.000 0.000 0.000 1.000;
> INFO: loading movable
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> Tmov: --------------------
> -1.600 0.000 0.000 128.000;
> 0.000 0.000 2.000 -80.000;
> 0.000 -1.600 0.000 128.000;
> 0.000 0.000 0.000 1.000;
> mkheaderreg = 1, float2int = 0
> Computing reg from header (and possibly input matrix)
> ---- Input registration matrix (computed) --------
> 0.997 -0.073 0.034 0.214;
> -0.046 -0.182 0.982 -30.911;
> -0.065 -0.981 -0.185 1.512;
> 0.000 0.000 0.000 1.000;
> ---------------------------------------
> ---- Input registration matrix --------
> 0.997 -0.073 0.034 0.214;
> -0.046 -0.182 0.982 -30.911;
> -0.065 -0.981 -0.185 1.512;
> 0.000 0.000 0.000 1.000;
> Determinant 1
> subject = ACC019
> RegMat ---------------------------
> 0.997 -0.073 0.034 0.214;
> -0.046 -0.182 0.982 -30.911;
> -0.065 -0.981 -0.185 1.512;
> 0.000 0.000 0.000 1.000;
> FSLOUTPUTTYPE NIFTI
> tkreg2FSL: mov det = -5.12001, ref det = -1
> Wed Apr 17 14:37:44 CEST 2013
> /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> flirt.fsl -ref
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> -in
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat
> -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0
> ** ERROR (nifti_image_read): failed to find header file for
> '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
> ** ERROR:
> nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister):
> bad header info
> ERROR: failed to open file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> ERROR: Could not open image
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> Image Exception : #22 :: Failed to read volume
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Abort (core dumped)
> Wed Apr 17 14:37:44 CEST 2013
> /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> flirt.fsl -ref
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> -in
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
> -init
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat
> -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
> ** ERROR (nifti_image_read): failed to find header file for
> '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
> ** ERROR:
> nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister):
> bad header info
> ERROR: failed to open file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> ERROR: Could not open image
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> Image Exception : #22 :: Failed to read volume
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Abort (core dumped)
> tkregister2_cmdl --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --fslreg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
> --noedit
> tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
> ERROR: cannot open
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
> cat:
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat:
> No such file or directory
> tmp: Subscript out of range.
>
> Started at Wed Apr 17 14:37:42 CEST 2013
> Ended at Wed Apr 17 14:37:44 CEST 2013
>
> fslregister Done
>
> To check results, run:
> tkregister2 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --surf orig
>
> mri_segreg --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --init-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --out-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
> --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
> --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
> regio_read_register(): No such file or directory
> Could not open
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> mri_segreg --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --init-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
> --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
> --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d
> 1e-3 --c0 0 --mincost
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.mincost
> --dof 6 --nmax 36 --param
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.param
> --surf white --cur-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.curopt.dat
> --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
> regio_read_register(): No such file or directory
> Could not open
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
> tkregister2_cmdl --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --noedit
> --ltaout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
> regio_read_register(): No such file or directory
> Could not open
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
> tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
> INFO: no target volume specified, assuming FreeSurfer orig volume.
> target volume orig
> movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> reg file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
> LoadVol 0
> ZeroCRAS 0
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
> ERROR: reading
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
> Cleaning up
>
> Started at Wed Apr 17 14:37:42 CEST 2013
> Ended at Wed Apr 17 14:37:45 CEST 2013
> BBR-Run-Time-Sec 3
>
> bbregister Done
> To check results, run:
> tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --surf
>
>
> mri_convert -at
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz
>
> mri_convert -at
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz
> ltaReadFile(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta):
> can't open file
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
> TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.996796, 0.0725774, -0.0336276)
> j_ras = (0.065149, 0.980551, 0.185135)
> k_ras = (-0.0464102, -0.182351, 0.982138)
> INFO: Reading transformation from file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta...
> Reading transform with LTAreadEx()
> No such file or directory
> ERROR: Reading transform from file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
> Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25
> 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s ACC019 exited with ERRORS at Wed Apr 17 14:37:45 CEST 2013
>
> For more details, see the log file
> /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/recon-all.log
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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