Hi,
We are just starting to run TBSS for the first time and are running into
some problems that we can't figure out. tbss_1_preproc seems to be running
fine, but when I move onto tbss_2_reg, I get the following errors (about 75%
of the time, and not specific to any particular subjects):
*************
tbss_2_reg -T
/bin/cp: cannot create regular file `FA/target.nii.gz': No such file or
directory
/usr/local/fsl/bin/tbss_2_reg: line 127: cd: FA: No such file or directory
K1013_dti_FA_FA_to_target K1015_dti_FA_FA_to_target K1016_dti_FA_FA_to_target
9302
*************
On the few instances in which I don't get those errors, when I move on to
tbss_3_postreg, I get the follwoing errors:
*************
tbss_3_postreg -S
using pre-chosen target for registration transforming all FA images into
MNI152 space K1013_dti_FA_FA
** ERROR (nifti_image_read): failed to find header file for
'K1013_dti_FA_FA_to_target_warp'
** ERROR: nifti_image_open(K1013_dti_FA_FA_to_target_warp): bad header info
Error: failed to open file K1013_dti_FA_FA_to_target_warp
ERROR: Could not open image K1013_dti_FA_FA_to_target_warp Image Exception :
#22 :: Failed to read volume K1013_dti_FA_FA_to_target_warp An error occured
while reading file: K1013_dti_FA_FA_to_target_warp K1015_dti_FA_FA
** ERROR (nifti_image_read): failed to find header file for
'K1015_dti_FA_FA_to_target_warp'
** ERROR: nifti_image_open(K1015_dti_FA_FA_to_target_warp): bad header info
Error: failed to open file K1015_dti_FA_FA_to_target_warp
ERROR: Could not open image K1015_dti_FA_FA_to_target_warp Image Exception :
#22 :: Failed to read volume K1015_dti_FA_FA_to_target_warp An error occured
while reading file: K1015_dti_FA_FA_to_target_warp K1016_dti_FA_FA
** ERROR (nifti_image_read): failed to find header file for
'K1016_dti_FA_FA_to_target_warp'
** ERROR: nifti_image_open(K1016_dti_FA_FA_to_target_warp): bad header info
Error: failed to open file K1016_dti_FA_FA_to_target_warp
ERROR: Could not open image K1016_dti_FA_FA_to_target_warp Image Exception :
#22 :: Failed to read volume K1016_dti_FA_FA_to_target_warp An error occured
while reading file: K1016_dti_FA_FA_to_target_warp 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
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
skeletonising mean FA
** ERROR (nifti_image_read): failed to find header file for 'mean_FA'
** ERROR: nifti_image_open(mean_FA): bad header info
Error: failed to open file mean_FA
ERROR: Could not open image mean_FA
Image Exception : #22 :: Failed to read volume mean_FA terminate called
after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/tbss_3_postreg: line 182: 21245 Aborted
$FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
now view mean_FA_skeleton to check whether the default threshold of 0.2
needs changing, when running:
tbss_4_prestats <threshold>
*************
If I then try to run fslview on the all_FA, it tells me that it could not
find the hdr or img files.
I have a feeling this is something simple that we're missing because we
haven't run TBSS before, but we just can't figure it out and any help would
be greatly appreciated.
|