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Hi - if you have just upgraded then I suggest starting from scratch. It sounds like your registration never completed. for some reason. Cheers. On 25 Feb 2009, at 06:45, Hanne Antila wrote: > 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 >> -------------------------------------------------------------------- >> ------- >> > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------