Input data format

The reconstruction programs read one ISMRMRD HDF5 file per run. It holds the k-space data and trajectories as ISMRMRD acquisitions, the maps the reconstruction needs as named NDArrays, and an XML header. FORGE Studio and Magneto's convertRecoInfoToIsmrmrd write files in this layout, and GenSyntheticISMRMRD writes a small synthetic example.

Header

FORGE reads these fields from the first encoding space. A file with more than one encoding space is refused.

Field	Used for
encodedSpace.matrixSize x, y, z	Image size, unless -x, -y or -z is given
reconSpace.fieldOfView_mm, or encodedSpace.fieldOfView_mm where that is zero	Voxel size in the NIfTI header (field of view divided by matrix size), unless --voxel-size is given. A zero field of view gives 1 mm.
encodingLimits	Number of shots, partitions, slices, repetitions, averages, echoes and cardiac phases (see below)

Acquisitions

Each acquisition is one readout for all coils. FORGE places it with these counters from the acquisition header:

Counter	Meaning in FORGE
kspace_encode_step_1	Shot
kspace_encode_step_2	Partition
slice	Slice
repetition	Repetition
average	Average
contrast	Echo
phase	Cardiac phase

The encodingLimits maximum of each counter sets how many there are. The reconstruction programs make one image for each combination of slice, repetition, average, echo and cardiac phase, and use every shot and partition of that combination as its data.

The trajectory of each acquisition has four rows:

Row	Content	Units
0	kx	cycles per field of view, in [−Nx/2, Nx/2)
1	ky	cycles per field of view, in [−Ny/2, Ny/2)
2	kz	cycles per field of view, in [−Nz/2, Nz/2). Zero for 2D.
3	Sample time, used for field correction	seconds

The acquisition's direction cosines and position give the image orientation in the NIfTI output. See Image orientation.

NDArrays

Each array is read as one flat vector. Images inside the arrays use FORGE's voxel order: y fastest, then x, then z.

Name	Type	Needed by	Content and layout
SENSEMap	complex double	all but gridCoilImages	Coil sensitivities. For each slice, all coils, coil slowest: Nx·Ny·Nz × Ncoils values per slice.
FieldMap	double	all but gridCoilImages	Off-resonance in rad/s, Nx·Ny·Nz values per slice
PhaseMaps	double	forgePcSense, forgePcSenseTimeSeg, oscillateRecon and their MPI versions	Phase of each shot in radians. One block of Nx·Ny·Nz × Nshots × Npartitions values per image, with blocks ordered slice fastest, then average, cardiac phase, echo and repetition.
v	complex double	oscillateRecon	The NRep × NRep temporal basis, column-major, one basis vector per column. The first --Rank columns are used.

Each name should appear once. If a file has more than one array with the same name, FORGE uses the first.

The programs apply each shot's phase map as exp(+i·PhaseMap) in the forward model.

Example files

GenSyntheticISMRMRD writes a small radial dataset in this layout, without v. See its entry in the command-line reference for its options.