nipreps/fmripost-phase

Processing steps

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  1. Collect data from preprocessing derivatives and raw dataset.
    • Raw phase data from raw dataset.
    • Preprocessed magnitude data from preprocessing derivatives.
    • Transforms from preprocessing derivatives.
  2. Rescale from arbitrary units to radians.
  3. Remove non-steady-state volumes?
  4. Unwrap phase data with ROMEO/MEDIC.
    • Combine unwrapped phase data across echoes with MEDIC?
  5. Calculate phase jump and phase jolt time series from rescaled, but not unwrapped, phase with LayNii's LN2_PHASE_JOLT.
  6. Extract confounds
  7. Denoise the phase data.
    • RETROICOR
  8. 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.

Related to nipreps/fmriprep#3336.