> I have a T1 weighted MR imaged acquired with aproximately 1x1x1
> resolution. It's got a .mat file with a rotation in it, and I want to
> reslice it to axial (analyze compatible) image at 1x1x1 resolution also.
>
> My one remaining question is what order of sinc interpolation to use.
> The default in the realign routine for functional data is a 9x9x9
> kernel. How should I compute what order sinc to use for interpolatin
> high resolution images?
It depends what you want to do with the data. If it is just for
visualisation then you dont need to use many neighbouring voxels. If you
want to create subtraction images then you would use more.
If you are merely rotating by multiples of 90 degrees and translating by
whole voxels then nearest neighbour interpolation will produce the same
results as sinc interpolation.
>
> The simplicstic answer is higher is better, except I've only got so many
> voxels and there's some noise in the image so I can't go too high.
> PS - how did John Ashburner et al arrive at 9x9x9 as the default for
> functional data motion correction?
It was a fine balance that I figured would minimise the number of complaints
about the realignment running too slowly while simultaneously minimising
objections about interpolation effects.
As our knowledge about the sources of the artifacts changes, then the methods
we use also evolve. For example, the view from the MR experts used to be
that most of the residual variance after realignment was from interpolation
artifact. Now, we know that much of it is due to motion by distortion
interraction (see Jesper's recent paper on the subject) and various other
interractions between image artifacts and movement, as well as the fact that
all slices are not acquired simultaneously.
The amount of residual variance in the images after realignment is probably
not an ideal indicator of the effects of using different interpolation
methods. We found that the residual variance after using trilinear
interpolation was actually less than that obtained using a good windowed
sinc. This was due to the smoothing introduced by using trilinear.
Best regards,
-John
--
Dr John Ashburner.
Wellcome Department of Cognitive Neurology.
12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420
http://www.fil.ion.ucl.ac.uk/~john
mail: [log in to unmask]
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