Hi,
On 14 Jun 2007, at 14:20, Ryan Muetzel wrote:
> Hello,
>
> I have a question concerning the input FA images for TBSS.
> Our group collects an axial DTI from a Siemens Trio machine. We
> convert the data to Analyze format using mri_convert and use FDT
> for DTI processing. After mri_convert, the data remain in
> radiological orientation (avworient -gerorient).
> When I run TBSS on this data, there are major alignment problems
> (over-warping), as seen in the stats directory with mean_fa and
> all_fa. However, if the original DTI data is first aligned to the
> MNI brain (6dof affine flirt) and then used as the input for TBSS,
> I no longer have problems with TBSS registration (ie all_fa and
> mean_fa look fine).
>
> My assumption is that the final areg, target to MNI transformation
> in tbss_3_postreg does not use a -180, 180 search, and thus is
> unable to properly register the data to the MNI brain. Is this
> correct?
>
> Any recommendations for input FA images (eg, use the 6 parameter
> flirt as described above, use avwswapdim
Yes - that! (avwswapdim, not FLIRT, to avoid interpolation)
Cheers.
> to properly orient the data to the MNI brain, etc).
>
> Thanks in advance for any help!
>
> -Ryan
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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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