Hi, it's unusual for the IRTK registration software to fail without
there being an obvious problem with the input data, so that's odd.
Could you send the data and we will have a look and maybe discuss
with the IRKT people at Imperial?
Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then email me the upload ID.
Thanks, Steve.
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
>
> ---------------------------------------------
> Mustafa Anjari
> Robert Steiner MR Unit
> Imaging Sciences Department
> Imperial College London
> Hammersmith Hospital
> Du Cane Road
> London W12 0HS
> UK
>
> Tel: +44 20 838 32336
> Email: [log in to unmask]
>
>
>
> On Mon, 1 Jan 2007 22:46:07 +0000, Christian Beckmann
> <[log in to unmask]> wrote:
>
>> Hi,
>>
>> difficult to say - did you maybe run out of disc space? tbss_2_reg is
>> just a simple shell script - if you're familiar with shell scripting
>> it should be straightforward to sort out how it works. If you want to
>> register just a single file the easiest is to simply run the script
>> again. If target.hdr exists the script will use the target. Also, it
>> will skip all blah_FAi.??? files for which there is a
>> blah_to_blah_nonlinear.msf file. Simply remove the msf file for the
>> one file that needs re-doing and all should be fine
>> cheers
>> christian
>>
>>
>> On 1 Jan 2007, at 17:33, Tal Herbsman wrote:
>>
>>> I just finished up TBSS non linear reg step (tbss_2_reg).
>>>
>>> For some reason there was not a subject_to_target_FAi_nonlinear.dof
>>> file
>>> generated for one of the subjects. the .msf file exists and there
>>> does not
>>> seem to have been a similar issue for any other registration for
>>> this or any
>>> other subjects (this subject was registered to every other subject
>>> just fine).
>>>
>>> Unfortunately I did not keep logs of the tbss_2_reg step. Any ideas
>>> how I
>>> can go ahead and debug this problem? Is there a quick way of
>>> reregistering
>>> just this subject to the specific target.
>>>
>>> Thanks,
>>>
>>> Tal.
>>>
>>> ---------
>>> Tal Herbsman, MD
>>> Psychiatry
>>> Medical University of South Carolina
>>
>> --
>> Christian F. Beckmann
>> Oxford University Centre for Functional
>> Magnetic Resonance Imaging of the Brain,
>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/
>> ~beckmann/
>> Phone: +44(0)1865 222551 Fax: +44(0)1865 222717
>> =====================================================================
>> ====
------------------------------------------------------------------------
---
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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