Can you verify that /usr/local/freesurfer/subjects/symmetry/lindsay/mri/brainmask.mgz exists? doug
On 03/25/2013 12:55 PM, Corinna Bauer wrote: > sure. Here is the dng.log. > > Corinna > > On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > Hi Corinna, can you run > > fslregister --debug --s lindsay --mov > hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1 > --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol > brainmask |& tee dng.log > > and send me the dng.log? > > doug > > > On 03/25/2013 12:39 PM, Corinna Bauer wrote: > > Hello all, > > > > I am attempting to run bbregister on 4D HARDI data that has already > > been motion, eddy, and epi-distortion corrected in fsl. I run > the command: > > bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz > --dti > > --init-fsl --reg register.dat and get a number of errors that > seem to > > begin in the mri_convert section as seen below. > > Any insight? > > > > Cheers, > > Corinna > > > > FREESURFER_HOME /usr/local/freesurfer > > mri_convert hardi/ffiltered_func_data_01.nii.gz > > ./tmp.bbregister.15356/template.nii > > mri_convert hardi/ffiltered_func_data_01.nii.gz > > ./tmp.bbregister.15356/template.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from hardi/ffiltered_func_data_01.nii.gz... > > TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-0.991204, -0.025762, 0.129811) > > j_ras = (-0.0259819, 0.999662, 0) > > k_ras = (0.129768, 0.00337275, 0.991539) > > writing to ./tmp.bbregister.15356/template.nii... > > fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii > > --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 > > --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol > > brainmask > > > > Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log > > > > Mon Mar 25 12:22:23 EDT 2013 > > --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg > > ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 > > --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol > > brainmask > > $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ > > lotfi > > Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC > > 2013 x86_64 x86_64 x86_64 GNU/Linux > > nIters 1 > > -------------------------------------- > > /usr/local/freesurfer/subjects/symmetry/lindsay > > mri_convert ERROR: could not determine file for > > /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: > > ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii > > mri_convert ERROR: could not determine file for > > /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: > > ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii > > > > mri_convert: extra arguments ("not" and following) > > > > type mri_convert -u for usage > > > > -------------------------------------- > > /usr/local/freesurfer/subjects/symmetry/lindsay > > mri_convert ./tmp.bbregister.15356/template.nii > > ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 > > mri_convert ./tmp.bbregister.15356/template.nii > > ./tmp.bbregister.15356/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 ./tmp.bbregister.15356/template.nii... > > TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-0.991204, -0.025762, 0.129811) > > j_ras = (-0.0259819, 0.999662, 0) > > k_ras = (0.129768, 0.00337275, 0.991539) > > keeping frame 0 > > writing to > ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii... > > Mov determinant is -6.125 > > /usr/local/freesurfer/subjects/symmetry/lindsay > > tkregister2_cmdl --mov > > ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg > > ./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader > > --fslregout ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay > > --noedit > > tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl > > INFO: no target volume specified, assuming FreeSurfer orig volume. > > target volume orig > > movable volume > ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii > > reg file ./tmp.bbregister.15356/fslregister/reg0.15393.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 > > /usr/local/freesurfer/subjects/symmetry/lindsay/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 > > ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii > > Tmov: -------------------- > > -1.750 0.000 0.000 112.000; > > 0.000 0.000 2.000 -60.000; > > 0.000 -1.750 0.000 112.000; > > 0.000 0.000 0.000 1.000; > > mkheaderreg = 1, float2int = 0 > > Computing reg from header (and possibly input matrix) > > ---- Input registration matrix (computed) -------- > > 0.991 0.026 -0.130 2.508; > > 0.130 0.003 0.992 -30.941; > > 0.026 -1.000 -0.000 1.279; > > 0.000 0.000 0.000 1.000; > > --------------------------------------- > > ---- Input registration matrix -------- > > 0.991 0.026 -0.130 2.508; > > 0.130 0.003 0.992 -30.941; > > 0.026 -1.000 -0.000 1.279; > > 0.000 0.000 0.000 1.000; > > Determinant 1 > > subject = lindsay > > RegMat --------------------------- > > 0.991 0.026 -0.130 2.508; > > 0.130 0.003 0.992 -30.941; > > 0.026 -1.000 -0.000 1.279; > > 0.000 0.000 0.000 1.000; > > FSLOUTPUTTYPE NIFTI > > tkreg2FSL: mov det = -6.125, ref det = -1 > > Mon Mar 25 12:22:34 EDT 2013 > > /usr/local/freesurfer/subjects/symmetry/lindsay > > flirt.fsl -ref > > ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in > > ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256 > > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 > -searchrz -90 > > 90 -verbose 0 -omat > > ./tmp.bbregister.15356/fslregister/fslmat0.trans.mat -schedule > > /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init > > ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 > > ** ERROR (nifti_image_read): failed to find header file for > > './tmp.bbregister.15356/fslregister/refvol.fslregister' > > ** ERROR: > > > nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister): > > bad header info > > ERROR: failed to open file > > ./tmp.bbregister.15356/fslregister/refvol.fslregister > > ERROR: Could not open image > > ./tmp.bbregister.15356/fslregister/refvol.fslregister > > Image Exception : #22 :: Failed to read volume > > ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii > > terminate called after throwing an instance of > 'RBD_COMMON::BaseException' > > Abort (core dumped) > > Mon Mar 25 12:22:34 EDT 2013 > > /usr/local/freesurfer/subjects/symmetry/lindsay > > flirt.fsl -ref > > ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in > > ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256 > > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 > -searchrz -90 > > 90 -verbose 0 -omat ./tmp.bbregister.15356/reg.init.dat.fsl.mat > -init > > ./tmp.bbregister.15356/fslregister/fslmat0.trans.mat -schedule > > /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch > > ** ERROR (nifti_image_read): failed to find header file for > > './tmp.bbregister.15356/fslregister/refvol.fslregister' > > ** ERROR: > > > nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister): > > bad header info > > ERROR: failed to open file > > ./tmp.bbregister.15356/fslregister/refvol.fslregister > > ERROR: Could not open image > > ./tmp.bbregister.15356/fslregister/refvol.fslregister > > Image Exception : #22 :: Failed to read volume > > ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii > > terminate called after throwing an instance of > 'RBD_COMMON::BaseException' > > Abort (core dumped) > > tkregister2_cmdl --s lindsay --mov > ./tmp.bbregister.15356/template.nii > > --reg ./tmp.bbregister.15356/reg.init.dat --fslreg > > ./tmp.bbregister.15356/reg.init.dat.fsl.mat --noedit > > tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl > > ERROR: cannot open ./tmp.bbregister.15356/reg.init.dat.fsl.mat > > cat: ./tmp.bbregister.15356/reg.init.dat: No such file or directory > > tmp: Subscript out of range. > > > > Started at Mon Mar 25 12:22:23 EDT 2013 > > Ended at Mon Mar 25 12:22:34 EDT 2013 > > > > fslregister Done > > > > To check results, run: > > tkregister2 --mov ./tmp.bbregister.15356/template.nii --reg > > ./tmp.bbregister.15356/reg.init.dat --surf orig > > > > mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg > > ./tmp.bbregister.15356/reg.init.dat --out-reg > > ./tmp.bbregister.15356/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 ./tmp.bbregister.15356/reg.init.dat > > mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg > > ./tmp.bbregister.15356/bbr.pass1.dat --out-reg register.dat --brute > > -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d > > 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param > > register.dat.param --surf white --cur-reg > > ./tmp.bbregister.15356/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 ./tmp.bbregister.15356/bbr.pass1.dat > > Cleaning up > > > > Started at Mon Mar 25 12:22:16 EDT 2013 > > Ended at Mon Mar 25 12:22:34 EDT 2013 > > BBR-Run-Time-Sec 18 > > > > bbregister Done > > To check results, run: > > tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg > > register.dat --surf > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <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. > > -- 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: 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
