Dear Gwenaëlle,
thank you for your help. I ran the analysis from the scratch (ok,
from tbss_1) just to be sure. It was really fast, but the scripts did
not generate anything in stats directory, only tons of error messages.
I am sending ls -la - I and errors. I hope it helps.
with thanks
George
2008/9/9 Gwenaëlle DOUAUD <[log in to unmask]>:
> 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 ...
>> >
>> >
>> >
>> >
>
>
>
>
