Hi,
This is a bug in the IRTK software - is there a reason why you're not
using the faster and (as of FSL 4.0) recommended option of registering
directly to the FMRIB58_FA? This hopefully should succeed. Otherwise
you could always find the _second_ most typical subject as the target
(look in all.msf) and maybe that would be a workaround? The next
release of FSL (hopefully some time before the autumn) will contain
FNIRT instead of IRTK, which won't have the same bug.
Cheers.
On 11 Mar 2008, at 19:55, Sara Moore wrote:
> 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
>>
>
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
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