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
----------------------------------------------------------------
--------
---
|