OK - I'm slightly guessing here, as Steve is away for Xmas, but here
goes.
Your mean_FA should not be A/P swapped wrt the MNI152, it should be
in the same orientation.
I guess what has happened is that your input files are A/P swapped.
The registration tool that tbss uses does not search for complete
reflections, or rotations as big as 180 degrees, so it has not found
the best match.
You can fix this by A/P swapping all of your input data. You can do
this with avwswapdim, either:
avwswapdim data x -y z data
or
avwswapdim data -x -y z data
depending on which one gives you the correct left-right orientation
(this depends on whether your A/P switch is a reflection or a rotation).
Then I'm afraid you will have to rerun all the registrations :(
Cheers
T
On 21 Dec 2006, at 22:12, Katherine Perdue wrote:
> Hello-
>
> I have run TBSS successfully (I think) except for one issue- when I
> look at MNI152.nii.gz and mean_FA.nii.gz in the stats/ directory,
> the two images are oriented differently (AP swap). How can I tell
> if my data is in MNI space (just has some unfortunate orientation
> issues) or if the alignment has completely failed? And if it has
> failed, any suggestions on how to fix it?
>
> Thanks,
> Katherine
>
>
>
> ++++++++++++++++++
> Katherine Perdue
> Research Assistant
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 02129
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