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Dear Steve Thank you very much for your answer, I am afraid that this could be the problem. I will try to redo the the TBSS analyses on the FA data with the newest version. >Hi - are you sure you're not mixing up previous versions of TBSS with >the latest in FSL4.1? TBSS analyses are not compatible across FSL4.1 >and previous versions of TBSS. > >Also, regarding: > >> (fslmerge -t dti4D_MD wd_* ). So I tried the following command; >> >> tbss_non_FA MD -nofslmerge > >Where does this option come from? I'm afraid that you can't just make >up options that don't exist, according to your desires! :-) It was worth trying it out;-) Best whishes Diana > >Cheers, Steve. > > > > >On 5 Nov 2008, at 10:20, Diana Wotruba wrote: > >> Dear all >> >> I would like to run TBSS on the mean diffusivity (MD). I ran >> tbss_non_FA MD >> in the TBSS directory followed by the steps as described below. I >> got the >> following notice of error: >> >> tbss_non_FA MD >> using pre-chosen registration target: dw_con_14_fa_FAi >> upsampling alternative images into standard space >> merging all upsampled MD 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_MD' >> ** ERROR: nifti_image_open(all_MD): bad header info >> Error: failed to open file all_MD >> Cannot open volume all_MD for reading! >> projecting all_MD onto mean FA skeleton >> ... >> >> >> Following the instructions, I did the TBSS analysis on the FA data, >> created >> a directory called MD in the TBSS analysis directory, copied the MD >> images >> in this directory and gave them the same name as the original FA >> volumes in >> origdata. >> >> It seems that merging all subjects' MD data into a 4D file stats/ >> all_MD >> didn't work. Yet it does work if I apply the fslmerge command by >> itself >> (fslmerge -t dti4D_MD wd_* ). So I tried the following command; >> >> tbss_non_FA MD -nofslmerge >> >> getting the same error message as described above. >> >> >> Thank you very much for your help >> Diana >> > > >--------------------------------------------------------------------------- >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 >---------------------------------------------------------------------------