Hi - from the top of the error messages it's clear that your OS
doesn't have the necessary system libraries installed to run the
nonlinear registration in TBSS. You could ask your sysad to install
those if possible - if not, you could wait a few weeks for the next
FSL release, which will not need those libraries.
Cheers.
On 7 May 2008, at 04:14, [log in to unmask] wrote:
> Dear Prof. Smith
> in the files tbss_2_reg.e*, I've found
> the following contents:
> I upload you the directory and I'll mail
> you the ID
> Thanks a lot
> Donatella Giuliani
>
>
>
> /usr/local/fsl/bin/DR/areg: error while loading shared libraries:
> libstdc++.so.5: cannot open shared object
> file: No such file or directory
> /usr/local/fsl/bin/DR/nreg: error while loading shared libraries:
> libstdc++.so.5: cannot open shared object
> file: No such file or directory
> /usr/local/fsl/bin/DR/dof2gipl: error while loading shared
> libraries: libstdc++.so.5: cannot open shared
> object file: No such file or directory
> /usr/local/fsl/bin/DR/dof2gipl: error while loading shared
> libraries: libstdc++.so.5: cannot open shared
> object file: No such file or directory
> ** ERROR (nifti_image_read): failed to find header file for 'grotNx'
> ** ERROR: nifti_image_open(grotNx): bad header info
> Error: failed to open file grotNx
> Cannot open volume grotNx for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'grotNy'
> ** ERROR: nifti_image_open(grotNy): bad header info
> Error: failed to open file grotNy
> Cannot open volume grotNy for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'grotNz'
> ** ERROR: nifti_image_open(grotNz): bad header info
> Error: failed to open file grotNz
> Cannot open volume grotNz for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'grotSx'
> ** ERROR: nifti_image_open(grotSx): bad header info
> Error: failed to open file grotSx
> Cannot open volume grotSx for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'grotSS'
> ** 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
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_reg: line 136: 13559 Aborted $FSLDIR/bin/
> fslstats grotSS M
> P
> 50
>> ../${I2R}_nonlinear.msf
> /usr/local/fsl/bin/DR/dof2gipl: error while loading shared
> libraries: libstdc++.so.5: cannot open shared
> object file: No such file or directory
> ** ERROR (nifti_image_read): failed to find header file for
> 'C119_PL_dti_FA_FAi_to_target_nonlineartmpX'
> ** ERROR:
> nifti_image_open(C119_PL_dti_FA_FAi_to_target_nonlineartmpX): bad
> header info
> Error: failed to open file C119_PL_dti_FA_FAi_to_target_nonlineartmpX
> Cannot open volume C119_PL_dti_FA_FAi_to_target_nonlineartmpX for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'C119_PL_dti_FA_FAi_to_target_nonlineartmpY'
> ** ERROR:
> nifti_image_open(C119_PL_dti_FA_FAi_to_target_nonlineartmpY): bad
> header info
> Error: failed to open file C119_PL_dti_FA_FAi_to_target_nonlineartmpY
> Cannot open volume C119_PL_dti_FA_FAi_to_target_nonlineartmpY for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'C119_PL_dti_FA_FAi_to_target_nonlineartmpZ'
> ** ERROR:
> nifti_image_open(C119_PL_dti_FA_FAi_to_target_nonlineartmpZ): bad
> header info
> Error: failed to open file C119_PL_dti_FA_FAi_to_target_nonlineartmpZ
> Cannot open volume C119_PL_dti_FA_FAi_to_target_nonlineartmpZ for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'C119_PL_dti_FA_FAi_to_target_nonlineartmpXX'
> ** ERROR:
> nifti_image_open(C119_PL_dti_FA_FAi_to_target_nonlineartmpXX): bad
> header info
> Error: failed to open file C119_PL_dti_FA_FAi_to_target_nonlineartmpXX
> Cannot open volume C119_PL_dti_FA_FAi_to_target_nonlineartmpXX for
> reading!
> /bin/rm: cannot remove `C119_PL_dti_FA_FAi_to_target_nonlineartmp*':
> No such file or directory
>
>
>
> ---------- Initial Header -----------
>
> From : "FSL - FMRIB's Software Library" [log in to unmask]
> To : [log in to unmask]
> Cc :
> Date : Sat, 3 May 2008 09:01:02 -0400
> Subject : Re: [FSL] TBSS
>
>
>
>
>
>
>
>> Hi,
>>
>> The registrations have not completed - there may be some useful
>> information in the tbss_2_reg.e* files. If this doesn't help you to
>> resolve what's happening, please upload the whole directory for us to
>> look at.
>>
>> 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.
>>
>>
>> Cheers.
>>
>>
>>
>> On 3 May 2008, at 05:53, [log in to unmask] wrote:
>>
>>> Dear Prof. Smith
>>> just few minutes later the execution of the command
>>> "tbss_2_reg -T" appears the number 13287
>>> and in the dir FAi are generated, as you can see
>>> from below, the files (attached with the e-mail)
>>> tbss_2_reg.e13287.1
>>> tbss_2_reg.e13287.2
>>>
>>> In the slicesdir are images of good quality
>>> Thanks for your attention
>>>
>>> Donatella Giuliani
>>>
>>> [giuliani@localhost TBSS_NEW]$ tbss_2_reg -T
>>> C117_GB_dti_FA_FAi_to_target
>>> C119_PL_dti_FA_FAi_to_target
>>> 13287
>>>
>>> [giuliani@localhost TBSS_NEW]$ ls
>>> FAi origdata
>>>
>>> [giuliani@localhost TBSS_NEW]$ cd FAi
>>> [giuliani@localhost FAi]$ ls lart
>>> total 15472
>>> rwrwr1
>>> giuliani giuliani 666792 May 2 09:54 C117_GB_dti_FA_FAi.img
>>> rwrwr1
>>> giuliani giuliani 348 May 2 09:54 C117_GB_dti_FA_FAi.hdr
>>> rwrwr1
>>> giuliani giuliani 666792 May 2 09:54 C119_PL_dti_FA_FAi.img
>>> rwrwr1
>>> giuliani giuliani 348 May 2 09:54 C119_PL_dti_FA_FAi.hdr
>>> drwxrwxrx
>>> 4 giuliani giuliani 4096 May 2 09:54 ..
>>> drwxrwxrx
>>> 2 giuliani giuliani 4096 May 2 09:54 slicesdir
>>> rwrwr1
>>> giuliani giuliani 0 May 2 09:56 tbss_2_reg.o13287.2
>>> rwrwr1
>>> giuliani giuliani 0 May 2 09:56 tbss_2_reg.o13287.1
>>> rwrwr1
>>> giuliani giuliani 3389 May 2 09:56 tbss_2_reg.e13287.2
>>> rwrwr1
>>> giuliani giuliani 3389 May 2 09:56 tbss_2_reg.e13287.1
>>> rwrwr1
>>> giuliani giuliani 14442064 May 2 09:56 target.img
>>> rwrwr1
>>> giuliani giuliani 348 May 2 09:56 target.hdr
>>> rwrwr1
>>> giuliani giuliani 108 May 2 09:56 .commands
>>> rwrwr1
>>> giuliani giuliani 0 May 2 09:56
>>> C119_PL_dti_FA_FAi_to_target_nonlinear.msf
>>> rwrwr1
>>> giuliani giuliani 0 May 2 09:56
>>> C117_GB_dti_FA_FAi_to_target_nonlinear.msf
>>> drwxrwxrx
>>> 3 giuliani giuliani 4096 May 2 09:56 .
>>> [giuliani@localhost FAi]$
>>>
>>>
>>>
>>>
>>>
>>>
>>> <tbss_2_reg.e13287.1><tbss_2_reg.e13287.2>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
---------------------------------------------------------------------------
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