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! :-)
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
>
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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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