---------- 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