Hi,
I'm wondering if there was a resolution found for the problem described in
the posts quoted below ("Re: randomise - tbss" on May 17th, 2007 and "Re:
TBSS registration problem." on March 6th, 2007) -- I'm having a similar
problem at the moment. I ran "tbss_2_reg -n" on 37 subjects (on an SGE
system, in case that is relevant), and 4 registrations did not complete.
These have empty *nonlinear.msf files, and the error log files contain this
error (followed by additional text that I can send along if necessary):
Numerical Recipes run-time error...
Singular matrix in routine ludcmp
...now exiting to system...
I tried both 1) manually running tbss_reg on the 4 pairs having the problem,
and 2) deleting the empty *nonlinear.msf files and rerunning "tbss_2_reg -n"
-- and both of these approaches resulted in the same error. Unfortunately,
one of the incomplete registrations contains the subject that tbss_3_postreg
tagged as the target image, and therefore "tbss_3_postreg -S" will not
complete. Is there a way to correct this error? I'd really like to be able
to use a target image from this population.
Thanks,
Sara Moore
Senior Research Specialist
Computation and Cognitive Neuroscience Lab
Emory University School of Medicine
On 17 May 2007, at 16:34, Suzanna Laycock wrote:
> Hi Steve,
>
> I did what you suggested, and got a number of error warnings. I've
> copied
> the whole list from the start as this will, undoubtedly, mean a lot
> more to
> you.
>
> Can you suggest anything?
>
> Best wishes
> Suzanna
>
> -----------------
> Image origin is 0 0 0
> X-axis is 1 0 0
> Y-axis is 0 1 0
> Z-axis is 0 0 1
> Range is from 0 to 12247
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx = 0.0000
> syz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Resolution level no. 3 (step sizes 20 to 2.5)
> Iteration = 1 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 80.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 2 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 60.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 3 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 60.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 4 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 40.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 5 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 20.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 6 (out of 20), step size = 20
> Numerical Recipes run-time error...
> Singular matrix in routine ludcmp
> ...now exiting to system...
> Reading target ... done
> Reading source ... done
> itkRigidTransformation::CheckHeader: Can't open file con_100887dti_FA_
> FAi_to_pat_99458dti_FA_FAi_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file con_100887dti_FA_
> FAi_to_pat_99458dti_FA_FAi_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file con_100887dti_FA_
> FAi_to_pat_99458dti_FA_FAi_nonlinear.dof
> ** ERROR: nifti_image_read(grotNx): can't open header file
> ** ERROR: nifti_image_open(grotNx): bad header info
> Error: failed to open file grotNx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNy): can't open header file
> ** ERROR: nifti_image_open(grotNy): bad header info
> Error: failed to open file grotNy
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNz): can't open header file
> ** ERROR: nifti_image_open(grotNz): bad header info
> Error: failed to open file grotNz
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSx): can't open header file
> ** ERROR: nifti_image_open(grotSx): bad header info
> Error: failed to open file grotSx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSS): can't open header file
> ** ERROR: nifti_image_open(grotSS): bad header info
> Error: failed to open file grotSS
> ERROR: Could not open image grotSS
> Image Exception : #22 :: Failed to read volume grotSS
> /usr/local/fsl/bin/tbss_reg: line 44: 3608 Aborted (c
> ore dumped) $FSLDIR/bin/avwstats++ grotSS -M -P 50 >../${I2R}_nonlinea
> r.msf
> processing pat_100809dti_FA_FAi_to_pat_99458dti_FA_FAi
> Reading target ... done
> Reading source ... done
> Target blurring is ... 0
> Target resolution is ... 0
> Source blurring is ... 0
> Source resolution is ... 0
> No. of resolution levels is ... 3
> No. of bins is ... 64
> No. of iterations is ... 20
> No. of steps is ... 4
> Length of steps is ... 5
> Similarity measure is ... CC
> Lambda 1 is ... 0
> Using 64 out of 64 bin(s) with width 192
> Using 64 out of 64 bin(s) with width 192
> Target image (reference)
> Image size is 128 128 70
> Voxel size is 1.75 1.75 2
> Image origin is 0 0 0
> X-axis is 1 0 0
> Y-axis is 0 1 0
> Z-axis is 0 0 1
> Range is from 0 to 12247
> Source image (transform)
> Image size is 128 128 70
> Voxel size is 1.75 1.75 2
> Image origin is 0 0 0
> X-axis is 1 0 0
> Y-axis is 0 1 0
> Z-axis is 0 0 1
> Range is from 0 to 12247
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx = 0.0000
> syz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Resolution level no. 3 (step sizes 20 to 2.5)
> Iteration = 1 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 80.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 2 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 60.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 3 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 60.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 4 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 120.0000 sz = 60.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 5 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 120.0000 sz = 40.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 6 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = -20.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 120.0000 sz = 40.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 7 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = -20.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 120.0000 sz = 20.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 8 (out of 20), step size = 20
> Numerical Recipes run-time error...
> Singular matrix in routine ludcmp
> ...now exiting to system...
> Reading target ... done
> Reading source ... done
> itkRigidTransformation::CheckHeader: Can't open file pat_100809dti_FA_
> FAi_to_pat_99458dti_FA_FAi_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file pat_100809dti_FA_
> FAi_to_pat_99458dti_FA_FAi_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file pat_100809dti_FA_
> FAi_to_pat_99458dti_FA_FAi_nonlinear.dof
> ** ERROR: nifti_image_read(grotNx): can't open header file
> ** ERROR: nifti_image_open(grotNx): bad header info
> Error: failed to open file grotNx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNy): can't open header file
> ** ERROR: nifti_image_open(grotNy): bad header info
> Error: failed to open file grotNy
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNz): can't open header file
> ** ERROR: nifti_image_open(grotNz): bad header info
> Error: failed to open file grotNz
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSx): can't open header file
> ** ERROR: nifti_image_open(grotSx): bad header info
> Error: failed to open file grotSx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSS): can't open header file
> ** ERROR: nifti_image_open(grotSS): bad header info
> Error: failed to open file grotSS
> ERROR: Could not open image grotSS
> Image Exception : #22 :: Failed to read volume grotSS
> /usr/local/fsl/bin/tbss_reg: line 44: 3328 Aborted (c
> ore dumped) $FSLDIR/bin/avwstats++ grotSS -M -P 50 >../${I2R}_nonlinea
> r.msf
> processing pat_100811dti_FA_FAi_to_pat_99458dti_FA_FAi
> Reading target ... done
> Reading source ... done
> Target blurring is ... 0
> Target resolution is ... 0
> Source blurring is ... 0
> Source resolution is ... 0
> No. of resolution levels is ... 3
> No. of bins is ... 64
> No. of iterations is ... 20
> No. of steps is ... 4
> Length of steps is ... 5
> Similarity measure is ... CC
> Lambda 1 is ... 0
> Using 64 out of 64 bin(s) with width 192
> Using 64 out of 64 bin(s) with width 192
> Target image (reference)
> Image size is 128 128 70
> Voxel size is 1.75 1.75 2
> Image origin is 0 0 0
> X-axis is 1 0 0
> Y-axis is 0 1 0
> Z-axis is 0 0 1
> Range is from 0 to 12247
> Source image (transform)
> Image size is 128 128 70
> Voxel size is 1.75 1.75 2
> Image origin is 0 0 0
> X-axis is 1 0 0
> Y-axis is 0 1 0
> Z-axis is 0 0 1
> Range is from 0 to 12247
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx = 0.0000
> syz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Resolution level no. 3 (step sizes 20 to 2.5)
> Iteration = 1 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 80.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 2 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 60.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 3 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 0.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 40.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 4 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 40.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 5 (out of 20), step size = 20
> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry = 20.0000 rz =
> 0.0000
> sx = 100.0000 sy = 100.0000 sz = 20.0000 sxy = 0.0000 syx = 0.0000 s
> yz = 0.0000
> szy = 0.0000 szx = 0.0000 sxz = 0.0000
> Iteration = 6 (out of 20), step size = 20
> Numerical Recipes run-time error...
> Singular matrix in routine ludcmp
> ...now exiting to system...
> Reading target ... done
> Reading source ... done
> itkRigidTransformation::CheckHeader: Can't open file pat_100811dti_FA_
> FAi_to_pat_99458dti_FA_FAi_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file pat_100811dti_FA_
> FAi_to_pat_99458dti_FA_FAi_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file pat_100811dti_FA_
> FAi_to_pat_99458dti_FA_FAi_nonlinear.dof
> ** ERROR: nifti_image_read(grotNx): can't open header file
> ** ERROR: nifti_image_open(grotNx): bad header info
> Error: failed to open file grotNx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNy): can't open header file
> ** ERROR: nifti_image_open(grotNy): bad header info
> Error: failed to open file grotNy
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNz): can't open header file
> ** ERROR: nifti_image_open(grotNz): bad header info
> Error: failed to open file grotNz
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSx): can't open header file
> ** ERROR: nifti_image_open(grotSx): bad header info
> Error: failed to open file grotSx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSS): can't open header file
> ** ERROR: nifti_image_open(grotSS): bad header info
> Error: failed to open file grotSS
> ERROR: Could not open image grotSS
> Image Exception : #22 :: Failed to read volume grotSS
> /usr/local/fsl/bin/tbss_reg: line 44: 3628 Aborted (c
> ore dumped) $FSLDIR/bin/avwstats++ grotSS -M -P 50 >../${I2R}_nonlinea
> r.msf
>
> Suzanna@suzanna ~/FSL_DATA/tbss
> $
On 6 Mar 2007, at 17:08, Mustafa Anjari wrote:
> Dear all
>
> I am having a similar problem running the tbss_2_reg script. Almost
> all the
> registrations worked correctly, but three did not finish (the
> source and
> target data were different in all three). In each case, there were no
> affine.dof and nonlinear.dof files and so an empty .msf file was
> generated.
> In each of these cases, the inverse transformation had worked
> without any
> errors.
>
> I thought it might be a memory problem, but when I reran the script
> with
> just these subjects (after deleting the appropriate .msf files) I
> got the
> following error messages
>
> vertex16 ma601 (../TBSS_GA/tmp): tbss_2_reg
> processing 230_TB-NNU38_dti_FAi_to_160_CR1132_dti_FAi
> Reading target ... done
> Reading source ... done
> .
> .
> .
> Iteration = 6 (out of 20), step size = 20
> Numerical Recipes run-time error...
> Singular matrix in routine ludcmp
> ...now exiting to system...
> Reading target ... done
> Reading source ... done
> itkRigidTransformation::CheckHeader: Can't open file
> 230_TB-NNU38_dti_FAi_to_target_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file
> 230_TB-NNU38_dti_FAi_to_target_affine.dof
> itkRigidTransformation::CheckHeader: Can't open file
> 230_TB-NNU38_dti_FAi_to_target_nonlinear.dof
> ** ERROR: nifti_image_read(grotNx): can't open header file
> ** ERROR: nifti_image_open(grotNx): bad header info
> Error: failed to open file grotNx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNy): can't open header file
> ** ERROR: nifti_image_open(grotNy): bad header info
> Error: failed to open file grotNy
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotNz): can't open header file
> ** ERROR: nifti_image_open(grotNz): bad header info
> Error: failed to open file grotNz
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSx): can't open header file
> ** ERROR: nifti_image_open(grotSx): bad header info
> Error: failed to open file grotSx
> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> ** ERROR: nifti_image_read(grotSS): can't open header file
> ** ERROR: nifti_image_open(grotSS): bad header info
> Error: failed to open file grotSS
> ERROR: Could not open image grotSS
> Image Exception : #22 :: Failed to read volume grotSS
> /poppy/homepublic/manjari/fsl/bin/tbss_reg: line 44: 12250 Aborted
> $FSLDIR/bin/avwstats++ grotSS -M -P 50 >../${I2R}_nonlinear.msf
>
> Any idea what I'm doing wrong? How easy would it be to register
> SubjectA-->SubjectB by generating the inverse of the SubjectB--
> >SubjectA
> transformation dof file? If I do this, how can I find the mean and
> median
> warping in order to create the .msf file?
>
> Thanks for your help,
> Mustafa
>
|
