Hi,
I'm a rookie in TBSS and I have run it successfully twice. However, now I
ran into some problems.
I first ran tbss_1_preproc *.nii.gz and tbss_2_reg -T as recommended and
everything seemed ok, no error messages.
The problems emerged, when I ran tbss_3_postreg -S. The error messages are
below. Has someone had similar problems? My data consists of 30 FA-images.
hanne@gyrus:~/DTI_Irina/TBBS$ tbss_3_postreg -S
using pre-chosen target for registration
transforming all FA images into MNI152 space
dti_FA_C01_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C01_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C01_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C01_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C01_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C01_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C02_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C02_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C02_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C02_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C02_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C02_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C03_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C03_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C03_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C03_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C03_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C03_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C04_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C04_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C04_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C04_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C04_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C04_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C06_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C06_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C06_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C06_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C06_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C06_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C07_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C07_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C07_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C07_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C07_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C07_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C09_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C09_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C09_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C09_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C09_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C09_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C10_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C10_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C10_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C10_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C10_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C10_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C12_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C12_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C12_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C12_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C12_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C12_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C13_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C13_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C13_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C13_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C13_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C13_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C14_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C14_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C14_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C14_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C14_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C14_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C15_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C15_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C15_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C15_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C15_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C15_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C16_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C16_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C16_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C16_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C16_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C16_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C17_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C17_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C17_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C17_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C17_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C17_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_C18_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_C18_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_C18_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_C18_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_C18_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_C18_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P01_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P01_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P01_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P01_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P01_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P01_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P02_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P02_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P02_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P02_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P02_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P02_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P03_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P03_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P03_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P03_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P03_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P03_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P04_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P04_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P04_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P04_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P04_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P04_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P05_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P05_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P05_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P05_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P05_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P05_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P06_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P06_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P06_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P06_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P06_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P06_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P07_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P07_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P07_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P07_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P07_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P07_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P08_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P08_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P08_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P08_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P08_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P08_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P10_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P10_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P10_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P10_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P10_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P10_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P11_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P11_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P11_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P11_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P11_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P11_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P12_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P12_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P12_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P12_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P12_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P12_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P13_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P13_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P13_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P13_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P13_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P13_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P14_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P14_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P14_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P14_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P14_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P14_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P15_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P15_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P15_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P15_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P15_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P15_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
dti_FA_P16_FAi
** ERROR (nifti_image_read): failed to find header file for
'dti_FA_P16_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(dti_FA_P16_FAi_to_target_nonlinear): bad header info
Error: failed to open file dti_FA_P16_FAi_to_target_nonlinear
ERROR: Could not open image dti_FA_P16_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
dti_FA_P16_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
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)
** 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
Error:: FslCloneHeader: Null pointer passed for FSLIO
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'
Aborted
now view mean_FA_skeleton to check whether the default threshold of 2000
needs changing, when running:
tbss_4_prestats [threshold]
hanne@gyrus:~/DTI_Irina/TBBS$
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