On Mon, Mar 25, 2013 at 1:47 PM, Corinna Bauer <corinnab83@gmail.com> wrote:

ahhh, yes, that's it. sorry my oversight.

On Mon, Mar 25, 2013 at 1:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Are you sure you made the right edit? It should be "--fsvol $fsvol.mgz" It looks like you might have changed it to "--fsvol.mgz $fsvol"

On 03/25/2013 01:30 PM, Corinna Bauer wrote:

Ok I adjusted the bbregister file to say fsvol.mgz in the location you specified and got this error a bit later on in the bbregister output:

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry
cd /usr/local/freesurfer/subjects/symmetry/lindsay
/usr/local/freesurfer/bin/bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat

$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
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
FREESURFER_HOME /usr/local/freesurfer
mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii
mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/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.15807/template.nii...
fslregister --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask
ERROR: Flag --fsvol.mgz unrecognized.
--s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask
mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/reg.init.dat --out-reg ./tmp.bbregister.15807/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.15807/reg.init.dat
mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/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.15807/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.15807/bbr.pass1.dat
Cleaning up

Started at Mon Mar 25 13:24:53 EDT 2013
Ended at Mon Mar 25 13:25:00 EDT 2013
BBR-Run-Time-Sec 7

bbregister Done
To check results, run:
tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat --surf

On Mon, Mar 25, 2013 at 1:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Corinna, can you edit $FREESURFER_HOME/bin/bbregister? If so,
change the following line

From
set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \
--niters 1 --maxangle 90 --tmp $tmpdir/fslregister \
--dof $FSLDOF --fsvol $fsvol)
To
set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \
--niters 1 --maxangle 90 --tmp $tmpdir/fslregister \
--dof $FSLDOF --fsvol $fsvol.mgz)

It is just the very last part that is changed where I added ".mgz"
to $fsvol

Re-run bbregister and let me know if this works.

doug

On 03/25/2013 01:11 PM, Corinna Bauer wrote:

yes, this file exists.

On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

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
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@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
>
>
>
>
>
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>
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--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
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<mailto:greve@nmr.mgh.harvard.edu
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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