Your First Reconstruction¶

SENSE / NUFFT¶

forgeSense \
    -i data.h5 \
    -o output/ \
    -F NUFFT \
    -t 4 \
    -n 20 \
    -B 0.001

Flag	Description
`-i`	Input ISMRMRD HDF5 file
`-o`	Output directory
`-F NUFFT`	Use NUFFT forward model
`-t 4`	Time segments for field correction
`-n 20`	CG iterations
`-B 0.001`	Regularization weight

pcSENSE (phase-corrected, multi-shot)¶

forgePcSense \
    -i data.h5 \
    -o output/ \
    -s 4 \
    -n 20 \
    -B 0.001

Monitoring with forgeview¶

Pipe reconstruction output to forgeview for real-time progress bars, convergence sparklines, and inline image preview:

forgeSense [args] 2>&1 | forgeview

For FORGE Studio integration (JSONL without spawning forgeview):

forgeSense [args] --no-tui

To redirect JSONL to a file or stdout:

forgeSense [args] --jsonl-output /path/to/output.jsonl
forgeSense [args] --jsonl-output stdout

For classic text output (no JSONL):

forgeSense [args] --no-jsonl

NIfTI Orientation Metadata¶

Output NIfTI files automatically include spatial orientation from the ISMRMRD acquisition headers (direction cosines, voxel sizes, position offsets). The ISMRMRD LPS coordinate system is converted to the NIfTI RAS convention, and both qform and sform are populated with NIFTI_XFORM_SCANNER_ANAT.

Override computed voxel sizes:

forgeSense [args] --voxel-size 1.5,1.5,3.0

Suppress orientation metadata (legacy identity behavior):

forgeSense [args] --no-orient