Output files

Images

The reconstruction programs write single-file NIfTI-1 images (.nii) with 32-bit float voxels. Each complex image becomes two files: a magnitude image ending in _mag.nii and a phase image, in radians, ending in _phs.nii.

Program	File names	Frames
forgeSense, forgePcSense, forgePcSenseTimeSeg and the MPI programs	img_Slice<s>_Rep<r>_Avg<a>_Echo<e>_Phase<p>_mag.nii and ..._phs.nii	One 3-D image per file
oscillateRecon	img_Slice<s>_Avg<a>_Echo<e>_Phase<p>_mag.nii and ..._phs.nii	One frame per repetition (4-D)
gridCoilImages	img_Rep<r>_Avg<a>_Echo<e>_Phase<p>_mag.nii and ..._phs.nii	One frame per coil (4-D), or slices × coils (5-D) when the file has several slices
gridCoilImages	imSOS_Rep<r>_Avg<a>_Echo<e>_Phase<p>.nii	Root sum of squares over coils

The counters start at 0. Files go in the -o directory.

Voxel order and header

Item	Value
dim[1], dim[2], dim[3]	Ny, Nx, Nz. FORGE stores images with y (the phase-encode direction) fastest, so NIfTI axis i is y.
pixdim[1..3]	Voxel size in mm along i, j, k: field of view over matrix size, or the --voxel-size values (y, x, z)
qform_code, sform_code	NIFTI_XFORM_SCANNER_ANAT (1), both describing the same affine
Affine	Axis i follows the acquisition's phase direction, j the read direction and k the slice direction, converted from ISMRMRD's LPS to NIfTI's RAS. The offset is the position of the centre of voxel (0, 0, 0).
scl_slope, scl_inter	1 and 0: the stored values are the image values
xyzt_units	mm

With --no-orient, qform_code and sform_code are 0 and the images carry voxel sizes only. When the acquisitions have no direction cosines, FORGE logs a warning and writes an identity orientation at the origin.

Image orientation explains how the affine is built. Versions before 0.14.0 swapped axes i and j in the affine, put the offset at the slab centre and set scl_slope to 100; see the changelog.

Log file

Every program writes a rotating log file, forge.log, in the current directory, whatever output mode is chosen.

Progress output

What the programs write to the terminal depends on the output options:

Options	Output
none	JSON lines on stderr. forgeview is started if stdout is a terminal and forgeview can be found.
--no-tui	JSON lines on stderr, and forgeview is never started
--jsonl-output stdout	JSON lines on stdout
--jsonl-output <file>	JSON lines written to the file
--no-jsonl	Plain log text on stderr and text progress bars, no JSON

The JSON lines are described in JSON lines protocol.