---------- Forwarded message ---------- From: Salil Soman salsoman@stanford.edu Date: Sat, May 25, 2013 at 8:00 PM Subject: BBR Register failing To: Douglas N Greve greve@nmr.mgh.harvard.edu
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 salsoman@stanford.edu Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu
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