[Neuroimaging] [DIPY] Re: DKI free water elimination

[Ping-Hong Yeh]

Hi Rafael,

 Thank you for the clarification.

Best,

Ping


On Fri, Aug 31, 2018 at 6:53 AM Rafael Henriques <rafaelnh21 at gmail.com>
wrote:

> Hi Ping,
>
> The code that you find in my pull request was intended to be integrated in
> Dipy. However, I decided to stop developing a free water DKI model fitting
> in Dipy, because I noticed that this dramatically compromises both
> precision and accuracy of kurtosis estimates.
>
> If you are interested in suppressing free water partial volume effect in
> your kurtosis measures, my alternative suggestion is to use the standard
> free water DTI Dipy's module to obtain a free water volume fraction map.
> Then you can use this map to remove the voxels of your kurtosis images that
> contain mostly free water (let's say f>0.5). This procedure will suppress
> the major free water partial volume contamination without compromising
> kurtosis precision and accuracy.
>
> More information: [Re] Optimization of a free water elimination
> two-compartment model for diffusion tensor imaging
> <https://github.com/ReScience-Archives/Henriques-Rokem-Garyfallidis-St-Jean-Peterson-Correia-2017/raw/master/article/Henriques-Rokem-Garyfallidis-St-Jean-Peterson-Correia-2017.pdf>
> .
>
> Best,
>
> Rafael
>
> >> Hi DIPY users,
> >>
> >> I would like to know whether there is a FW-DKI module in DIPY.
> >> I came across  Rafael's free water DKI,
> >>
> >> https://github.com/RafaelNH/free-water-DKI/blob/master/fwDKI.py
> >>
> >> Is this compatible with the current DIPY package? Any comments in using
> this >> module?
> >>
> >> Thank you.
> >>
> >> Ping
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