Hi,
I thought about that and updated to the newest version. Unfortunately
this didn'n help and the problem remains the same. So I guess the
registration is then the issue here and now when I think about it, the
registration did finish really fast. It isn't the data anyway, since I
already tried with different dataset.
The FA file contains these kinds of files
Best.mfs
Subject_FA.nii.gz
Subject_FA_mask.nii.gz
subject_FA_to_target_warp.mfs
target.nii.gz
Those subject_FA_to_target_warp.mfs -files are size 0 bites and empty
when viewed in gedit. Does someone has any pointers? All help will be
appreciated!
Hanne Antila
[log in to unmask]
0500-563674
----- Original Message -----
From: Steve Smith <[log in to unmask]>
Date: Tuesday, February 24, 2009 10:36 pm
Subject: Re: [FSL] problem with TBSS/tbss_3_postreg
To: [log in to unmask]
> 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
> --------------------------------------------------------------------
> -------
>
|