Processing steps
Opened this issue · 1 comments
tsalo commented
- 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 from rescaled, but not unwrapped, phase with LayNii's LN2_PHASE_JOLT.
- Extract confounds
- HighCor
- Phase quality map calculation (Rodriguez et al., 2010)
- Denoise the phase data.
- RETROICOR
- 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.
tsalo commented
Useful links:
- https://neurostars.org/t/processing-for-complex-valued-fmri-data/5093
- https://github.com/tsalo/complex-flow (a past attempt at something similar)