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-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 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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.mal...@student.unimelb.edu.au<mailto:c.mal...@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 > > > _______________________________________________ > 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 gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
