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Hi,
I'm an IT from the University of Rome (La Sapienza) and actually I'm working
at the department of neurology. We've got a lot of trouble using fsl
(expecially the tbss software). I have tried to set up tbss on debian (etch
and lenny) and ubuntu (feisty and gutsy) using official and unofficial
packages (Michael Hanke).

In every machine (32 bit) we have:

- fsl package from your repository
- fsl-atlases from your repository
- fslview from your repository
- itk manually dowloaded and installed under /usr/local
- . /ect/fsl/fsl.sh globally set in /etc/bash.bashrc
- itk binaries in PATH (should we need a license for this ?)
- /bin/sh is a symbolic link to /bin/bash (NOT dash)

tbss_1_preproc CON_N00300_dti_data_FA.nii.gz CON_N00302_dti_data_FA.nii.gz
seems to work (it creates hdr and img files under FAi directory and moves
nii files under origdata).

tbss_2_reg -T seems to have problems (the process runs just for few seconds
and two empty msf files are created under FAi directory:
CON_N00300_dti_data_FA_FAi_to_target_nonlinear.msf and
CON_N00302_dti_data_FA_FAi_to_target_nonlinear.msf).

Finally, tbss_3_postreg -S crashes with this output:

/usr/lib/fsl/tbss_3_postreg: line 96: cd: FAi: No such file or directory
using pre-chosen target for registration
transforming all FA images into MNI152 space
CON_N00300_dti_data_FA_FAi
** ERROR (nifti_image_read): failed to find header file for
'CON_N00300_dti_data_FA_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(CON_N00300_dti_data_FA_FAi_to_target_nonlinear):
bad header info
Error: failed to open file CON_N00300_dti_data_FA_FAi_to_target_nonlinear
ERROR: Could not open image CON_N00300_dti_data_FA_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
CON_N00300_dti_data_FA_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/tbss_3_postreg: line 148: 11552 Abortito               
$FSLDIR/bin/applywarp -i $f -o ${f}_to_target_nonlinear_hr -r target -w
${f}_to_target_nonlinear --rel
CON_N00302_dti_data_FA_FAi
** ERROR (nifti_image_read): failed to find header file for
'CON_N00302_dti_data_FA_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(CON_N00302_dti_data_FA_FAi_to_target_nonlinear):
bad header info
Error: failed to open file CON_N00302_dti_data_FA_FAi_to_target_nonlinear
ERROR: Could not open image CON_N00302_dti_data_FA_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
CON_N00302_dti_data_FA_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/tbss_3_postreg: line 148: 11553 Abortito               
$FSLDIR/bin/applywarp -i $f -o ${f}_to_target_nonlinear_hr -r target -w
${f}_to_target_nonlinear --rel
merging all upsampled FA images into single 4D image

Usage: fslmerge <-x/y/z/t/a> <output> <file1 file2 .......>
     -t : concatenate images in time
     -x : concatenate images in the x direction
     -y : concatenate images in the y direction
     -z : concatenate images in the z direction
     -a : auto-choose: single slices -> volume, volumes -> 4D (time series)
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Error:: FslCloneHeader: Null pointer passed for FSLIO
creating valid mask and mean FA
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
skeletonising mean FA
** ERROR (nifti_image_read): failed to find header file for 'mean_FA'
** ERROR: nifti_image_open(mean_FA): bad header info
Error: failed to open file mean_FA
ERROR: Could not open image mean_FA
Image Exception : #22 :: Failed to read volume mean_FA
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/tbss_3_postreg: line 190: 11588 Abortito               
$FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
now view mean_FA_skeleton to check whether the default threshold of 2000
needs changing, when running:
tbss_4_prestats [threshold]


Is this a sort of bug ?

Thank you for your help.