urrrgh - I'm pretty sure this is a bug in the IRTK software
- but hopefully if this has not happened too many times you can get
around it.
If you just try running tbss_3_postreg, hopefully it will choose a
target subject for whom all the subjectN_to_chosentarget.msf files
exist....note which target it chooses and then test that all the
relevant .msf files are complete.
Cheers, Steve.
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
> $
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library
> [mailto:[log in to unmask]] On Behalf Of Steve Smith
> Sent: 16 May 2007 16:24
> To: [log in to unmask]
> Subject: Re: [FSL] randomise
>
>
> Hi - sounds like some of them failed - I suggest that you find the
> empty .msf files
> ls -l *.msf
> and delete the empty ones, then just run tbss_2_reg again and it will
> only do the missing registrations.
>
> Cheers.
>
>
>
> On 16 May 2007, at 15:50, Suzanna Laycock wrote:
>
>> Thanks Steve...should have noticed that.
>>
>> I've gone back and looked at the files I have, and I was wondering
>> if I
>> could check the following with you.
>>
>> I have two groups of 9, so tbss_2_reg should generate 324 files.
>>
>> But it hasn't, 24 of the files seem to be missing, even though the
>> script
>> ended.
>>
>> I take it this isn't normal? Do you have any suggestions why this
>> happened?
>> I don't want to start re-running the script as it took 10 days to
>> complete,
>> if we're going to get the same problem.
>>
>> Best wishes
>> Suzanna
>>
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf Of Steve Smith
>> Sent: 14 May 2007 16:24
>> To: [log in to unmask]
>> Subject: Re: [FSL] randomise
>>
>>
>> Your model has 18 timepoints but your data only has 15! Steve.
>>
>>
>> On 14 May 2007, at 16:21, Suzanna Laycock wrote:
>>
>>> Hi Steve,
>>>
>>> It says the following:
>>>
>>> Suzanna@suzanna ~/FSL_DATA/tbss/stats
>>> $ avwinfo all_FA_skeletonised
>>> data_type
>>> dim1 182
>>> dim2 218
>>> dim3 182
>>> dim4 15
>>> datatype 16
>>> pixdim1 -1.0000000000
>>> pixdim2 1.0000000000
>>> pixdim3 1.0000000000
>>> pixdim4 1.0000000000
>>> cal_max 0.0000
>>> cal_min 0.0000
>>> glmax 0
>>> glmin 0
>>> origin1 91
>>> origin2 127
>>> origin3 73
>>> file_type ANALYZE-7.5
>>>
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>> Behalf Of Steve Smith
>>> Sent: 11 May 2007 15:19
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] randomise
>>>
>>>
>>> What does
>>> avwinfo all_FA_skeletonised
>>> say?
>>>
>>>
>>>
>>> On 11 May 2007, at 14:35, Suzanna Laycock wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm trying to run the last part of tbss - randomise, and I get the
>>>> following error message. Any suggestions why? I have 9 control
>>>> and
>>>> 9 patient subjects. Below is the design.mat and design.con
>>>> files.
>>>>
>>>> Suzanna@suzanna ~/FSL_DATA/tbss/stats
>>>> $ design_ttest2 design 9 9
>>>>
>>>> Suzanna@suzanna ~/FSL_DATA/tbss/stats
>>>> $ randomise -i all_FA_skeletonised -o tbss -m mea
>>>> n_FA_skeleton_mask
>>>> -d design.mat -t design.con -n 5000 -c 3 -V 48620 permutations
>>>> required for exhaustive test number of rows in design matrix
>>>> doesn't
>>>> match numb er of "time points" in input data!
>>>>
>>>>
>>>> My design.mat is:
>>>>
>>>> /NumWaves 2
>>>> /NumPoints 18
>>>> /PPheights 1 1
>>>> /Matrix
>>>> 1 0
>>>> 1 0
>>>> 1 0
>>>> 1 0
>>>> 1 0
>>>> 1 0
>>>> 1 0
>>>> 1 0
>>>> 1 0
>>>> 0 1
>>>> 0 1
>>>> 0 1
>>>> 0 1
>>>> 0 1
>>>> 0 1
>>>> 0 1
>>>> 0 1
>>>> 0 1
>>>>
>>>> And my design.con is:
>>>>
>>>> /NumWaves 2
>>>> /NumContrasts 2
>>>> /PPheights 1 1
>>>> /Matrix
>>>> 1 -1
>>>> -1 1
>>>>
>>>
>>>
>>> ----------------------------------------------------------------
>>> --------
>>> ---
>>> 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
>>> ----------------------------------------------------------------
>>> --------
>>> ---
>>
>>
>> ----------------------------------------------------------------
>> --------
>> ---
>> 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
>> ----------------------------------------------------------------
>> --------
>> ---
>
>
> ----------------------------------------------------------------
> --------
> ---
> 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
> ----------------------------------------------------------------
> --------
> ---
------------------------------------------------------------------------
---
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
------------------------------------------------------------------------
---
|