Calibration passes

OpenKSpace runs a fixed sequence of calibration passes before the reconstruction strategy proper. Each pass can be disabled individually via a CLI flag or ReconConfig field; the order is fixed and cannot be re-ordered.

Noise pre-whitening

Per-coil noise covariance estimated from the dedicated noise scans in the file, decomposed via Cholesky, and applied as a whitening transform to all image-domain acquisitions (Kellman & McVeigh 2005). Disable with --no-prewhiten if your file has no noise scans.

Navigator-echo phase correction

For sequences that include ACQ_IS_PHASECORR_DATA lines (EPI-style navigator echoes), OpenKSpace estimates the linear phase per coil and applies the inverse to imaging lines, removing N/2 ghosting. Disable with --no-phasecorr.

Readout oversampling removal

Standard 2x readout oversampling is removed by IFFT along kx and cropping the central half in image space, then optionally re-FFTing if a downstream strategy requires k-space. Disable with --no-oversampling-removal.

Partial-Fourier homodyne

For acquisitions with partial-Fourier ky sampling, the missing high-frequency data is reconstructed via homodyne filtering (Noll 1991; McGibney 1993). Disable with --no-partial-fourier.

FOV crop

Final image-space crop to the encoded FOV. Disable with --no-crop.