Fix the image geometry

FORGE writes the orientation of each image into the NIfTI header from the ISMRMRD acquisition headers (see Image orientation). This page covers the cases where that needs adjusting.

The voxel size is wrong

The voxel size is the field of view in the ISMRMRD header divided by the matrix size. If the header's field of view is missing or wrong, or you reconstruct at a different matrix size than the header describes, set the voxel size yourself:

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

The three values are the read (x), phase-encode (y) and slice (z) sizes in mm. FORGE writes them to NIfTI axes j, i and k, because axis i is the phase-encode direction (see Output files).

You want images without orientation

Some older pipelines expect FORGE images without an affine. Add --no-orient:

forgeSense [options] --no-orient

The files then have voxel sizes but qform_code and sform_code of 0.

Images from before 0.14.0 overlay wrongly

FORGE 0.14.0 fixed the NIfTI geometry. Older files swapped axes i and j in the affine, put the offset at the slab centre, and stored scl_slope = 100, so viewers that apply the slope showed values 100 times too large. The voxel data did not change.

To fix an old file, reconstruct it again with 0.14.0 or later. Any script that corrected for the old affine or divided by the old slope must be updated at the same time.

The image is in the wrong place or flipped

Check the input first. FORGE reads read_dir, phase_dir, slice_dir and position from the first acquisition of each slice, in ISMRMRD's LPS patient coordinates. If FORGE logs All direction cosines are zero; falling back to identity orientation, the file has no orientation and the images are written at the origin with an identity affine. Fix the data preparation so it writes these fields.