Hi- this is a very old version of FSL / TBSS.  I recommend installing the latest version. Cheers. 

--------------------
Stephen M. Smith,  Professor of Biomedical Engineering
Associate Director,   Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington,
Oxford. OX3 9 DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]
http://www.fmrib.ox.ac.uk/~steve
----------------------

On 10 Jan 2011, at 09:20, "PD Dr. Lutz Lüdemann" <[log in to unmask]> wrote:

Hi Stephen,

until now, we do not used SGE and the parameters SGE_root and SGE_cell are not set.

but the log file tbss_2_reg.e9303.1 provides some information, that the filed areg, and nreg dof2gipl were not found:

/usr/share/fsl/bin/tbss_reg: line 105: /usr/share/fsl/bin/DR/areg: Datei oder Verzeichnis nicht gefunden
/usr/share/fsl/bin/tbss_reg: line 115: /usr/share/fsl/bin/DR/nreg: Datei oder Verzeichnis nicht gefunden
/usr/share/fsl/bin/tbss_reg: line 124: /usr/share/fsl/bin/DR/dof2gipl: Datei oder Verzeichnis nicht gefunden
/usr/share/fsl/bin/tbss_reg: line 125: /usr/share/fsl/bin/DR/dof2gipl: Datei oder Verzeichnis nicht gefunden
** 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

Maybe, tbss is still using the old version.

But I can´t really follow the  fsl_app_wrapper:

 ls -l /usr/bin/fsl4.1-tbss_2_reg
 /usr/bin/fsl4.1-tbss_2_reg -> ../lib/fsl/4.1/fsl_app_wrapper


And the old configuration parameters are still set:

FSLDIR=/usr/share/fsl
FSLTCLSH=/usr/share/fsl/bin/fsltclsh
FSLWISH=/usr/share/fsl/bin/fslwish
FSLBROWSER=/usr/share/fsl/tcl/fslwebbrowser
FSLCONFDIR=/usr/share/fsl/config
FSL_DIR=/usr/share/fsl
FSL_BIN=/usr/share/fsl/bin

Should the following shell commands anymore used?

        setenv FSLDIR /usr/share/fsl
        source $FSLDIR/etc/fslconf/fsl.conf
        setenv LD_LIBRARY_PATH "${LD_LIBRARY_PATH}:/usr/lib/fsl"
        setenv PATH       "${PATH}:/usr/lib/fsl"

Best Regards,
Lutz


Stephen Smith schrieb:
[log in to unmask]" type="cite">Hi - maybe you have SGE partially/wrongly setup?   Are there any useful messages in the *.o and *.e log files?
Cheers.


On 7 Jan 2011, at 18:37, PD Dr. Lutz Lüdemann wrote:

Hi Stephen,

I got after several seconds the output of the time and no process is anymore working. That seems to be the main problem, the registration is not performed and I get no error message, only empty registration parameter files for all images.


Best Regards,

Lutz

Stephen Smith schrieb:
[log in to unmask]" type="cite">Hi - are you sure you waited for stage 2 to finish running?
Cheers.


On 7 Jan 2011, at 17:51, PD Dr. Lutz Lüdemann wrote:

Hello Methew,

I dated up fsl to the latest available debian version but the error is the same:

fsl4.1-tbss_1_preproc *.nii.gz
Using multiplicative factor of 10000
processing pro01_dti_FA
processing pro02_dti_FA
processing pro03_dti_FA
processing pro04_dti_FA
processing pro05_dti_FA
processing pro06_dti_FA
processing pro07_dti_FA
processing pro08_dti_FA
processing pro09_dti_FA
processing pro10_dti_FA
processing pro11_dti_FA
processing pro12_dti_FA
Now running "slicesdir" to generate report of all converted images
Finished. To view, point your web browser at


fsl4.1-tbss_2_reg -T
pro01_dti_FA_FAi_to_target
pro02_dti_FA_FAi_to_target
pro03_dti_FA_FAi_to_target
pro04_dti_FA_FAi_to_target
pro05_dti_FA_FAi_to_target
pro06_dti_FA_FAi_to_target
pro07_dti_FA_FAi_to_target
pro08_dti_FA_FAi_to_target
pro09_dti_FA_FAi_to_target
pro10_dti_FA_FAi_to_target
pro11_dti_FA_FAi_to_target
pro12_dti_FA_FAi_to_target
2477

 ls -al FAi/
insgesamt 25856
   624  7. Jan 2011  .commands
   348  7. Jan 2011  pro01_dti_FA_FAi.hdr
984312  7. Jan 2011  pro01_dti_FA_FAi.img
     0  7. Jan 2011  pro01_dti_FA_FAi_to_target_nonlinear.msf

Note, that the file pro01_dti_FA_FAi_to_target_nonlinear.msf is empty!

fsl4.1-tbss_3_postreg -S
using pre-chosen target for registration
transforming all FA images into MNI152 space
pro01_dti_FA_FAi
** ERROR (nifti_image_read): failed to find header file for 'pro01_dti_FA_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(pro01_dti_FA_FAi_to_target_nonlinear): bad header info
Error: failed to open file pro01_dti_FA_FAi_to_target_nonlinear
ERROR: Could not open image pro01_dti_FA_FAi_to_target_nonlinear

Best Regards,

Lutz

Matthew Webster schrieb:
[log in to unmask]" type="cite"> 
Hello Lutz,
		   It looks like you are using an old version of FSL ( the current version is 4.1.6 ) - we would strongly recommend updating to the latest version before continuing..

Many Regards

Matthew
  
Hi,

I have installed fsl using the actual debian destribution 4.04 and got the following error message when using 

tbss_3_postreg -S
using pre-chosen target for registration
transforming all FA images into MNI152 space
pro01_dti_FA_FAi
** ERROR (nifti_image_read): failed to find header file for 'pro01_dti_FA_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(pro01_dti_FA_FAi_to_target_nonlinear): bad header info
Error: failed to open file pro01_dti_FA_FAi_to_target_nonlinear
ERROR: Could not open image pro01_dti_FA_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume pro01_dti_FA_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/share/fsl/bin/tbss_3_postreg: line 148: 11870 Abgebrochen             $FSLDIR/bin/applywarp -i $f -o ${f}_to_target_nonlinear_hr -r target -w ${f}_to_target_nonlinear --rel

The error message was independent of the option. I found, that the file with the registration data, pro01_dti_FA_FAi_to_target_nonlinear.msf,  was empty: 

-rw-r--r--       348 2011-01-06 20:55 pro01_dti_FA_FAi.hdr
-rw-r--r--  984312 2011-01-06 20:55 pro01_dti_FA_FAi.img
-rw-r--r--           0 2011-01-07 12:19 pro01_dti_FA_FAi_to_target_nonlinear.msf

I concluded, that the registration was not performed.

I tried to execute the command manually:

/usr/share/fsl/bin/tbss_reg pro01_dti_FA_FAi target

and got the following error message, that the follwing files were not found:

/usr/share/fsl/bin/tbss_reg: line 105: /usr/share/fsl/bin/DR/areg: Datei oder Verzeichnis nicht gefunden
/usr/share/fsl/bin/tbss_reg: line 115: /usr/share/fsl/bin/DR/nreg: Datei oder Verzeichnis nicht gefunden
/usr/share/fsl/bin/tbss_reg: line 124: /usr/share/fsl/bin/DR/dof2gipl: Datei oder Verzeichnis nicht gefunden
/usr/share/fsl/bin/tbss_reg: line 125: /usr/share/fsl/bin/DR/dof2gipl: Datei oder Verzeichnis nicht gefunden

and indeed, the folder /usr/share/fsl/bin/DR does not exist.

But the current distribution does not include the folder.

Is there any solution for the problem?

Thank You,
Lutz Lüdemann

Charité, Berlin




---------------------------------------------------------------------------
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
---------------------------------------------------------------------------





<lutz.luedemann.vcf>


---------------------------------------------------------------------------
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
---------------------------------------------------------------------------





-- 


  PD Dr. Lutz Lüdemann
  Universitätsklinikum Charité
  Campus Virchow-Klinikum
  Klinik für Strahlentherapie
  Medizinische Physik 
  Augustenburger Platz 1
  13353 Berlin
  Telefon: (49) 030/450-557188
  Telefax: (49) 030/450-557939
  email: [log in to unmask]
<lutz.luedemann.vcf>