search

nipreps / fmripost-phase

An attempt at an fMRIPost workflow for handling phase data
Apache License 2.0
2 stars 1 forks source link

NORDIC? #10

Open tsalo opened 2 months ago

tsalo commented 2 months ago

The main questions are:

  1. Will fMRIPrep incorporate NORDIC? If so, then there's no need to implement it in fMRIPost-Phase.
  2. Does NORDIC meaningfully impact preprocessing (i.e., motion parameters, boldref space)? If so, then we really need it in fMRIPrep. Otherwise, we can apply it to the raw data in fMRIPost-Phase, then run STC, and then apply the transforms from fMRIPrep.

Related issues/PRs: https://github.com/SteenMoeller/NORDIC_Raw/pull/21, https://github.com/nipreps/fmriprep/issues/3308.

tsalo commented 1 month ago

Even if we add NORDIC to fMRIPrep, it won't output processed phase data, so we need to run NORDIC with the same parameters in fMRIPost-Phase to get the denoised phase data, right? Assuming NORDIC actually modifies the phase data of course.

tsalo commented 1 month ago

@mattcieslak had the great idea to test out the effect of NORDIC on motion parameters by simulating data with POSSUM, although he already found that MP-PCA had a large effect on dMRI motion parameters and I'm betting that extends to fMRI.