HI - I'm guessing that means that the input data may not have had
valid NIFTI headers?
If the FSL page about formats
http://www.fmrib.ox.ac.uk/fsl/fsl/formats.html
and the FAQ don't help, use fslswapdim etc. to get all your input data
into the same orientation as the MNI standard space images, making
sure not to get L-R swapped wrongly. Check in FSLView that the
apparent orientation, and the labels, are all the same as the MNI
images.
Once this is all done, hopefully you should have no further problems
with the TBSS scripts?
Cheers.
On 8 Sep 2009, at 11:41, Laurence O'Dwyer wrote:
> Hi,
> I have two queries about tbss:
> (1)After running a number of preliminary tbss runs I’m continuing to
> have
> problems with the orientation of the images after tbss_2_reg – all
> images
> are incorrectly labelled with P in anterior areas and A in Posterior
> areas.
> Overlaying the MNI shows that tbss_2_reg images are reversed in
> relation to
> MNI. I’m still unsure why this is happening and how to correct it.
> (2)Once the stats folder is created, how is it possible to calculate
> the
> mean global FA values for each group, i.e. for control and patient
> group? I
> presume this should be a straightforward procedure but I can’t find
> any
> reference to it in the tbss manual.
>
> Thanks,
> Laurence
>
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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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