[Mrtrix-discussion] SIFT: normalise to the b0 image

[Robert Smith]

Hi Jan,

This is an important point, and one that we sometimes forget that we (as
in, the MRtrix dev team) think about quite differently to others in
Diffusion MR.
We will draw attention to this issue in an upcoming publication, but I'll
try to give a succinct explanation here.

Conventionally, the log-transform with respect to the b=0 image converts a
signal amplitude to an apparent diffusion coefficient; nothing
controversial here. However if you were to then apply a spherical
deconvolution transform, the FOD amplitude along a particular direction
would be proportional to the ADC of the fibre population oriented along
that direction. This isn't particularly useful information; it doesn't tell
us much about differences between fibre populations throughout the image,
or indeed within a voxel.

Ideally what we actually want for a number of applications is the volume of
each fibre population element, in all voxels throughout the image. Based on
David Raffelt's early simulations
<http://www.sciencedirect.com/science/article/pii/S1053811911012092>, it
turns out that (under certain conditions) the radial component of the DWI
signal amplitude is actually a pretty decent marker for intra-cellular
volume. Therefore, by ignoring the b=0 images completely and just running
SD on the raw DWI intensities, we get pretty useful biological information
and interpretation from the FOD; we also conveniently bypass the issue of
Gibbs ringing in the b=0 images. Caveat is that you need a uniform B1 field
(i.e. intensity bias field correction); for applications like AFD you also
need inter-subject intensity normalisation, but that's not necessarily a
problem for SIFT depending on how you're using it.

That's all for now. Hope that clarifies why we choose to apply SD in this
way; in fact, this approach dates all the way back to the original SD paper.
Rob


--

*Robert Smith, Ph.D*
Research Officer, Imaging Division

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au

On Sat, Dec 13, 2014 at 1:37 AM, Jan Schreiber <schreiber at cbs.mpg.de> wrote:
>
> Dear MRtrix Team,
>
> thank you very much for this great software and for making it freely
> available!
>
> In your publication "SIFT: Spherical-deconvolution informed filtering of
> tractograms" you state
>
> "The diffusion signal must not be normalised to the b = 0 image
> intensity. This preserves the linearity of the spherical deconvolution
> transform between the measured DW signal and the resulting FOD."
>
> Shouldn't we preserve the linearity of the spherical deconvolution
> transform between the FOD and the DW _signal attenuation_ rather than
> the DW _signal_?
>
> Thanks,
> Jan
>
>
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