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Collect data from preprocessing derivatives and raw dataset.
Raw phase data from raw dataset.
Preprocessed magnitude data from preprocessing derivatives.
Transforms from preprocessing derivatives.
Rescale from arbitrary units to radians.
Remove non-steady-state volumes?
Unwrap phase data with ROMEO/MEDIC.
Combine unwrapped phase data across echoes with MEDIC?
Calculate phase jump and phase jolt time series with LayNii's LN2_PHASE_JOLT.
Extract confounds (if any can be extracted).
Apply transforms from fMRIPrep to get data into the appropriate spaces.
Probably need to ignore STC.
In idevicente/Phase-based_denoising_pipeline, they combine mag + phase into complex, then split into real + imag, then apply the transforms, then combine into complex, then split into mag + phase. Not sure if that's necessary.
idevicente/Phase-based_denoising_pipeline
, they combine mag + phase into complex, then split into real + imag, then apply the transforms, then combine into complex, then split into mag + phase. Not sure if that's necessary.Related to nipreps/fmriprep#3336.
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