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

[Thijs Dhollander]

Hi Scott,

Interesting issue this is indeed! So to summarise what you are reporting
(just to make sure I'm getting it right): you're seeing hyperintense voxels
at b=3000 in the MS lesion, but the ADC map shows no clear decrease in
values compared to surrounding (supposedly healthy) WM tissue, is that
correct?  Are you sure there's not even a slight decrease in ADC?  Due to
the log-transform, it might be hard to spot; definitely try to increase the
contrast in your viewer to investigate the area.  I'm not an expert on MS,
but doing a few searches, I seem to run into articles describing actual
increased restriction in certain (stages of) MS lesions (presenting ADC
maps with hypointense lesions.

Let's say you would indeed be observing no decrease in ADC at all, yet a
clear increase in b=3000 DWI values, that would mean an obvious increase in
value of the b=0 image(s): are you seeing that as well in the data at hand?

If the latter is true, I think I can potentially help you out with these
partial volume issues (over time).  I notice you're at Unimelb.  I'm
working at the Florey (in Heidelberg, but mobile and in the Parkville area
at times); we should have a coffee and a chat some time, and take a good
hands-on look at those data you're sitting on. ;-)

Cheers,
Thijs


On 20 January 2016 at 14:54, Scott Cameron Kolbe <kolbes at unimelb.edu.au>
wrote:

> Dear Donald, Rob and Dave
>
> Just found this discussion whilst going through the archives. Sorry to
> bring it up again but I’ve been having similar concerns to Jan recently
> whilst working on multiple sclerosis data. The T2 “shine-through” effect
> that Jan is referring to in MS results from T2 signal enhancement that is
> not related to changes in CSF volume fraction.  Therefore hyperintense
> voxels in DWI, considered by SD to be highly restricted diffusion, are in
> fact not that different from surround tissue on the ADC map.
>
> This problem might be solved by acquiring low-B images for normalisation
> where freely diffusing fluid is essentially annulled but even lightly
> restricted water is not. However, we are sitting on quite a bit of data
> with only b=0 or b=3000. Do you think partial volume correction might be
> possible?
>
> cheers
> Scott
>
>
> Scott Kolbe
> kolbes at unimelb.edu.au
>
>
>
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