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 ...
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