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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