Hi Matt (and Andreas),
> I have used this on a few datasets, and was satisfied that the
> correction
> produced fewer problems than the original distortion.
I think the phrase "fewer problems than the original distortion" is
important here.
When fnirt was developed I didn't think it would be possible to use
for this purpose, but when people reported that they had tried it with
some success I did some tests too. As Matt says, it produces results
that at least visually are better than the often quite horrific
distortions one sees in diffusion images. However, the contrast is
quite different in FA and T1 images, and in particular the high
intensity "tracts" in the FA images are typically limited to the
centres of the white matter areas. This means that one can often see
that fnirt attempts to "widen" these tracts, which I think might be
quite bad in many applications.
It would be _much_ better to perform a proper distortion correction
based either on a fieldmap or on blip-up-blip-down data (for which
software is now being tested in house), and therefore I would like to
discourage people from thinking that they can skip collecting those
extra data and simply use fnirt instead.
Jesper
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