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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 > -------------------------------------------------------------------- > ------- >