CLI quickstart

Inspect a file

openkspace info  scan.h5    # print header metadata
openkspace probe scan.h5    # scan acquisition index ranges

Reconstruct (defaults)

openkspace recon scan.h5

By default this writes PNGs of every slice into recon_out/ using the IFFT + root-sum-of-squares strategy and all calibration passes auto-detected from the data.

Choose a reconstruction strategy

openkspace recon scan.h5 --strategy ifft-rss
openkspace recon scan.h5 --strategy grappa
openkspace recon scan.h5 --strategy sense  --sense-maps espirit
openkspace recon scan.h5 --strategy cs

Common options

openkspace recon scan.h5 \
    --out my_out/ \
    --slice 12 \
    --strategy sense --sense-maps walsh \
    --sense-gfactor --write-gfactor \
    --format both

Flag	Effect
--out <dir>	Output directory (default recon_out/)
--slice <N>	Reconstruct one slice only
--fft auto|2d|3d	FFT mode (default auto)
--format png|nifti|both	Output format (default png)
--no-prewhiten	Skip noise pre-whitening
--no-phasecorr	Skip navigator phase correction
--no-oversampling-removal	Keep 2x kx samples
--no-partial-fourier	Skip homodyne
--no-crop	Keep full oversampled FOV
--pct-low <f> --pct-high <f>	Contrast window percentiles

See the CLI reference for the full strategy-specific flag set (GRAPPA kernel sizes, SENSE map sources, CS regulariser, etc.).