Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <[email protected]>wrote: > Hi Sal, can you post this to the list instead of me directly? > thanks! > doug > > > > On 5/25/13 11:00 PM, Salil Soman wrote: > > Dear Doug, > > I attempted to run the process we discussed earlier today for registering > a different tissue contrast to the T1 after freesurfer 5.3 was run. > > I had run an FSSPGR for my subject using the following command: > > recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm > -openmp 50 -hippo-subfields -all > > It finished without any problems. > > Then I tried running the bbrregister command: > > bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg > register.dat --bold > > (this version was with bold contrast, but I get the same error if I try > t1 or t2). > > The process fails and I get the following error log (below). Any > suggestions on what I am doing wrong? > > Thanks, > > Sal > > ---------- Forwarded message ---------- > From: Salil Soman <[email protected]> > Date: Sat, May 25, 2013 at 7:54 PM > Subject: bbregister fail log > To: [email protected] > > > Logfile for bbregister > Sat May 25 19:51:15 PDT 2013 > > setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS > cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov > QSM_906.nii.gz --init-fsl --reg register.dat --bold > > $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ > Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 > 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer > mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii > mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from QSM_906.nii.gz... > TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0.313177, 0.949695) > k_ras = (0, -0.949695, 0.313177) > writing to ./tmp.bbregister.26724/template.nii... > fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii > --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 > --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol > brainmask > > Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log > > Sat May 25 19:51:17 PDT 2013 > --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg > ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov > --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask > $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ > corn18.stanford.edu > Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 > 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > nIters 1 > -------------------------------------- > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > > mri_convert: extra arguments ("not" and following) > > type mri_convert -u for usage > > -------------------------------------- > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > mri_convert ./tmp.bbregister.26724/template.nii > ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 > mri_convert ./tmp.bbregister.26724/template.nii > ./tmp.bbregister.26724/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.26724/template.nii... > TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0.313177, 0.949695) > k_ras = (0, -0.949695, 0.313177) > keeping frame 0 > writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... > Mov determinant is -0.984886 > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > tkregister2_cmdl --mov > ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg > ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout > ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit > tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii > reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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.26724/fslregister/movvol.fslregister.nii > Tmov: -------------------- > -1.000 0.000 0.000 112.000; > 0.000 0.000 0.985 -83.715; > 0.000 -1.000 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) -------- > 1.000 -0.000 -0.000 1.591; > -0.000 -0.950 0.313 0.719; > 0.000 -0.313 -0.950 -5.896; > 0.000 0.000 0.000 1.000; > --------------------------------------- > ---- Input registration matrix -------- > 1.000 -0.000 -0.000 1.591; > -0.000 -0.950 0.313 0.719; > 0.000 -0.313 -0.950 -5.896; > 0.000 0.000 0.000 1.000; > Determinant 1 > subject = WMR3T_0015z_FS > RegMat --------------------------- > 1.000 -0.000 -0.000 1.591; > -0.000 -0.950 0.313 0.719; > 0.000 -0.313 -0.950 -5.896; > 0.000 0.000 0.000 1.000; > FSLOUTPUTTYPE NIFTI > tkreg2FSL: mov det = -0.984886, ref det = -1 > Sat May 25 19:51:22 PDT 2013 > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 > -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat > -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init > ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 > ** ERROR (nifti_image_read): failed to find header file for > './tmp.bbregister.26724/fslregister/refvol.fslregister' > ** ERROR: > nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): > bad header info > ERROR: failed to open file > ./tmp.bbregister.26724/fslregister/refvol.fslregister > ERROR: Could not open image > ./tmp.bbregister.26724/fslregister/refvol.fslregister > Image Exception : #22 :: Failed to read volume > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Abort > Sat May 25 19:51:22 PDT 2013 > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 > -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init > ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule > /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch > ** ERROR (nifti_image_read): failed to find header file for > './tmp.bbregister.26724/fslregister/refvol.fslregister' > ** ERROR: > nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): > bad header info > ERROR: failed to open file > ./tmp.bbregister.26724/fslregister/refvol.fslregister > ERROR: Could not open image > ./tmp.bbregister.26724/fslregister/refvol.fslregister > Image Exception : #22 :: Failed to read volume > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Abort > tkregister2_cmdl --s WMR3T_0015z_FS --mov > ./tmp.bbregister.26724/template.nii --reg > ./tmp.bbregister.26724/reg.init.dat --fslreg > ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit > tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl > ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat > cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory > tmp: Subscript out of range. > > Started at Sat May 25 19:51:17 PDT 2013 > Ended at Sat May 25 19:51:23 PDT 2013 > > fslregister Done > > To check results, run: > tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg > ./tmp.bbregister.26724/reg.init.dat --surf orig > > mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg > ./tmp.bbregister.26724/reg.init.dat --out-reg > ./tmp.bbregister.26724/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.26724/reg.init.dat > mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg > ./tmp.bbregister.26724/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.26724/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.26724/bbr.pass1.dat > Cleaning up > > Started at Sat May 25 19:51:15 PDT 2013 > Ended at Sat May 25 19:51:24 PDT 2013 > BBR-Run-Time-Sec 9 > > bbregister Done > To check results, run: > tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf > > > 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. >
_______________________________________________ Freesurfer mailing list [email protected] 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.
