HI - are you maybe mixing up FSL versions? *_FAi images are from the
old version. Either that or the registrations didn't complete correctly.
Cheers.
On 24 Feb 2009, at 12:53, Hanne Antila wrote:
> 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$
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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