Hi George,
I am not 100% sure of what's happening here, but I have a bad feeling...
Could you please re-run tbss_2 and 3 after replacing all the `$FSLDIR/bin/imglob by `$FSLDIR/bin/remove_ext in these two scripts? And please get back to me to tell me if it's working or not...
It seems that Ubuntu platforms have got troubles dealing with our command imglob (also in FSL-VBM), with this kind of subsequent problems.
Cheers,
Gwenaelle
--- En date de : Mar 9.9.08, Jiří Keller, M.D. <[log in to unmask]> a écrit :
> De: Jiří Keller, M.D. <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] tbss_3_postreg problem in new FSL version
> À: [log in to unmask]
> Date: Mardi 9 Septembre 2008, 15h55
> ls -al, compressed using tar.gz (I hope attachments are
> allowed) ...
>
> 2008/9/9 Gwenaëlle DOUAUD
> <[log in to unmask]>:
> > Hi George,
> >
> > could you please copy/paste the output of an ls -al in
> your FA directory?
> >
> > Thanks,
> > Gwenaelle
> >
> >
> > --- En date de : Ven 5.9.08, Jiří Keller, M.D.
> <[log in to unmask]> a écrit :
> >
> >> De: Jiří Keller, M.D.
> <[log in to unmask]>
> >> Objet: [FSL] tbss_3_postreg problem in new FSL
> version
> >> À: [log in to unmask]
> >> Date: Vendredi 5 Septembre 2008, 18h43
> >> Hi,
> >> I am trying to re-run my dataset after upgrading
> FSL
> >> using Ubuntu
> >> 7.10 packages from FA.nii.gz files. I am sorry for
> long
> >> mail, but I
> >> would like to include as much info as possible.
> >>
> >> tbss_3_postreg - S outputs on standard output:
> >>
> >> --snip--
> >> originalfilename_FA.nii.gz_FA_mask.nii.gz
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz
> >> originalfilename_FA.nii.gz_FA.nii.gz
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz
> >> --snip--
> >>
> >> (lines above for each patient)
> >>
> >> --snip--
> >> 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)
> >> creating valid mask and mean FA
> >> skeletonising mean FA
> >> now view mean_FA_skeleton to check whether the
> default
> >> threshold of
> >> 0.2 needs changing, when running:
> >> tbss_4_prestats <threshold>
> >> --snip--
> >>
> >> Which looks like some error in fslmerge calling
> routine.
> >> Error log has 35 kB (!) and is full of messages
> like:
> >>
> >> --snip--
> >> ** ERROR (nifti_image_read): failed to find header
> file for
> >>
> 'originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz_to_target_warp'
> >> ** ERROR:
> >>
> nifti_image_open(originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz_to_target_warp):
> >> bad header info
> >> Error: failed to open file
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> ERROR: Could not open image
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> Image Exception : #22 :: Failed to read volume
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> An error occured while reading file:
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> ** ERROR (nifti_image_read): failed to find header
> file for
> >>
> 'originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz_to_target_warp'
> >> ** ERROR:
> >>
> nifti_image_open(originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz_to_target_warp):
> >> bad header info
> >> Error: failed to open file
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> ERROR: Could not open image
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> Image Exception : #22 :: Failed to read volume
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> An error occured while reading file:
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz_to_target_warp
> >> --snip--
> >>
> >> FA directory contains
> >> for each patient:
> >> --list--
> >> originalfilename_FA.nii.gz_FA_mask.nii.gz
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target.mat
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target.nii.gz
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.msf
> >>
> originalfilename_FA.nii.gz_FA_mask.nii.gz_to_target_warp.nii.gz
> >> originalfilename_FA.nii.gz_FA.nii.gz
> >> originalfilename_FA.nii.gz_FA.nii.gz_to_target.mat
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target.nii.gz
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.msf
> >>
> originalfilename_FA.nii.gz_FA.nii.gz_to_target_warp.nii.gz
> >> originalfilename_FA_to_target.log
> >> --list--
> >> and best.msf
> >> and 2*patient_count of tbss_2_reg.o8740.* files
> >>
> >> All files seem to have reasonable size (non-zero),
> I am
> >> able to open
> >> them in fslview.
> >> Any help would be very appreciated.
> >>
> >> with thanks
> >> George
> >>
> >> P.S.: Analyze of these files (the same set)
> succeeded (but
> >> with
> >> incorrect registration :-( ) in FSL 4.0 ...
> >
> >
> >
> >
|