Hi Suren,
Replying back on list: No problem. You might want to be careful with
Gaussian filtering of the data. It's definitely not the best way to denoise
DWI data. You might want to look into some of the other methods implemented
in DIPY, like the recently added patch2self method:
https://dipy.org/documentation/1.4.1./examples_built/denoise_patch2self/#exa...
Cheers,
Ariel
On Tue, Oct 19, 2021 at 7:41 PM Surendra Maharjan <suren634634@gmail.com>
wrote:
Hello Ariel,
Thank you very much. We sorted out the issue. Thanks for the advice. We
were missing Gaussian filtering.
Many Thanks,
Suren
Sent from my iPhone
On Oct 19, 2021, at 12:28 PM, Ariel Rokem <arokem@uw.edu> wrote:
Hi Suren,
Thanks for your email. Can you tell us more about the data? What b-values
are you using? What is the spatial resolution? What instrument is this
collected on? Also, what processing do you do with the data before you
analyze it with DKI? Any denoising? Also, what do you mean that the "FA is
high in some areas"? Are these values aphysical? It might be helpful to
plot the signal in some of the voxels in which you are seeing surprising FA
values as a function of the b-value. It might help track down what is going
on.
Cheers,
Ariel
On Tue, Oct 19, 2021 at 8:11 AM Maharjan, Surendra <smaharj@iu.edu> wrote:
Hello Dipy Developers,
My name is Surendra Maharjan (Suren) from Indiana University-Purdue
University Indianapolis (IUPUI), Indianapolis. I am using Dipy for DKI
analysis of exvivo mouse brain. I would be grateful if you kindly suggest
some optimization for the DKI analysis. The kurtosis FA map has very high
values at some areas.
kfa
<image001.png>
Many Thanks,
Suren
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Ariel Rokem