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-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 > > > > > -- > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
