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 ...
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