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Add optional NORDIC denoising step #3308
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Would be good to know how NORDIC fits into the fit and transform workflows. Does it need to be done before/after HMC/STC? Is it deterministic/nondeterministic? What's the runtime? Is there a compact set of parameters that can be saved, or is it basically just the noRF files are the parameters? |
Pinging @madisoth for his thoughts, but my understanding is that it needs to be done before HMC, STC, or basically anything else. I don't think it's deterministic, unfortunately. Most parameters are determined from the data (e.g., how many noise volumes, whether there's phase data or not). The only one I can think of that users might want to vary is Not sure about the runtime since I've only ever run it on large numbers of runs in jobs. |
Just popping in to say that re the MATLAB implementation, I recently found this package with a python implementation of NORDIC: https://paquiteau.github.io/patch-denoising/ (and associated paper: https://hal.science/hal-03895194/file/isbi2023_denoise.pdf) I did not have a chance to try it myself (or NORDIC itself), so buyer beware. |
Thanks @mvdoc! The repo looks really promising, and even if it's not completely up-to-date with I also wanted to note that, for multi-echo data, NORDIC could be run on each echo independently (which I believe is how most folks do it), or we could try the HYDRA-OC approach from this OHBM abstract by Marco Flores-Coronado and Cesar Caballero-Gaudes. In that approach, it looks like you concatenate the multi-echo in a spatial direction (Z in their case), run NORDIC, and then split up the denoised data. |
I looked at the |
I think we might need to use the MATLAB version. @Remi-Gau do you know any tricks for using MATLAB in containers/BIDS apps? |
Yeah. Make sure the code is Octave compatible and use Octave. |
This one is the one I was planning to use, since it's the one others seem to be using. I don't know if it's Octave-compatible though. It does rely on the |
What would you like to see added in fMRIPrep?
If possible, it would be great to support NORDIC denoising.
NORDIC is currently written in MATLAB, which might be a problem.
Do you have any interest in helping implement the feature?
Yes
Additional information / screenshots
BIDS now supports separate
noRF
scans for the no-excitation pulse volumes people often acquire at the ends of their runs for NORDIC.The text was updated successfully, but these errors were encountered: