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-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] en nom de Eduard Vilaplana Martinez
> [evilapl...@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-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] en nom de Charles Malpas
> [c.mal...@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
> <ni...@nmr.mgh.harvard.edu<mailto:ni...@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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>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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>>
>>
>
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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.mal...@student.unimelb.edu.au<mailto:c.mal...@student.unimelb.edu.au>
> Skype: charles.malpas
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Warren Winter
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Boston Children's Hospital
Sheridan Laboratory of Cognitive Neuroscience
Division of Developmental Medicine
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