This issue has come up before, and I’m not sure we have a good answer to it… I think this is going to require some investigation before we can settle the matter, but someone will need to invest the time to do this, and that’s in very short supply these days.
Here are a few posts where the issue has been discussed:
Hi,
I am just updating our diffusion processing pipeline to include the dwidenoise and mrdegibbs steps. Our raw data is organised in two DICOM directories, one containing the main diffusion-weighted data, and one containing reversed phase-encode data. I am wondering whether I am ok to perform the dwidenoise and mrdegibbs steps only on the main diffusion volume only? Or should I also run the steps on the reversed phase-encode series?
Many thanks,
Hanne Stotesbury
omit the denoising step from processing of just that set of volumes
What set of volumes are you referring to here?
This is in reference to whatever set of images are to be provided to FSL topup via the -se_epi option. But the wording is maybe clumsy; that’s me trying to avoid writing an essay in every thread :-/
Let’s suppose the situation is (as it sounds applies to your case), that you have:
Phase encoding AP: 1 b=0, 60 b=3000 volumes;
Phase encoding PA: 1 b=0.
, and the tools you …
Dear All,
Here are some (very) basic/naive dwi preprocessing questions, please let me know if you have any thoughts on these.
I have two sets acquired sequentially within the same scan session (each set contains 10 Xb=0 images acquired first in the respective set, then 60 dwi b=3000; 1st set PA, 2nd set AP encode direction, 2x2x2 mm resolution)
dwidenoise
re influence of PE direction on noise, if any: should one apply denoising to each set separately then combine outputs, or combine both s…
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