Hi George,
you just need to wait till the completion of tbss_2_reg step :-)! Your non-linear registrations are not completed (wait for dti_cx1_FA_to_target.nii.gz and
dti_cx1_FA_FA_to_target_warp.nii.gz to be created).
Now you've got another problem: you also need to change from imglob to remove_ext in your tbss_1_preproc script.
So start again from scratch, and wait for the 2nd step to be completed before moving to the third one...
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, 18h38
> 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
> ...
> >> >
> >> >
> >> >
> >> >
> >
> >
> >
> >
