NIfTI & NRRD Volumetric Medical Imaging (.nii, .nrrd, .nhdr)

@modelscript/nifti (languages/nifti) provides native WebAssembly parsing, $4\times 4$ qform quaternion and sform affine Right-Anterior-Superior (RAS) coordinate transformation validation, anatomical segmentation labelmap volume calculation, Marching Tetrahedra 3D iso-surface mesh extraction, DAEBuilder lowering, and ISO 10303-21 STEP / OpenSCAD projections for NIfTI-1 / NIfTI-2 and NRRD (Nearly Raw Raster Data) medical imaging volumes.

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Supported Extensions & Standards

Extension	Format	Description
.nii	NIfTI-1 / NIfTI-2	Neuroimaging & clinical volumetric format encoding 3D/4D voxel grids, pixdim spacings, and qform/sform RAS affines
.nrrd, .nhdr	Teem / 3D Slicer NRRD	Nearly Raw Raster Data header/volume with space directions, space origin, and anatomical segmentation labelmaps

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Key Capabilities

1. Voxel-to-RAS Affine Geometry & Orientation Auditing

• Parses voxel dimensions $(N_x,N_y,N_z,N_t)$, millimeter spacings $(\mathrm{\Delta }x,\mathrm{\Delta }y,\mathrm{\Delta }z)$, unit quaternion parameters $(b,c,d)$ with qfac $\in \{-1,+1\}$, and $4\times 4$ sform homogeneous transformation matrices ${\mathbf{T}}_{\text{voxel}\to \text{RAS}}$.
• Detects singular affine matrices ($det({\mathbf{M}}_{3\times 3})=0$), left-right radiological/neurological handedness mismatches between qform and sform, and anisotropic slice gaps.

2. Segmentation Labelmaps & Marching Tetrahedra Iso-Surfacing

• Extracts organ and tumor volumes (${\text{mm}}^3$ / ${\text{cm}}^3$), bounding boxes, and centroids for segmented ROIs, and triangulates watertight 3D surface meshes (extractIsoSurfaceMesh).

3. CAD Reconstruction (STEP AP242 & OpenSCAD)

• Projects extracted anatomical iso-surfaces directly into ISO 10303-21 STEP B-Rep shells (niftiToStep) and OpenSCAD polyhedron(...) CSG modules (niftiToScad) for patient-specific implant and surgical guide design.

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Pre-Flight Diagnostics

10 rules8 error2 warning

Code	Rule	Severity	Message
M9501	nifti-invalid-dimensions	error	Invalid NIfTI/NRRD volume dimensions: dim[0]='<ndim>', spatial size=(<nx>, <ny>, <nz>).
M9502	nifti-non-positive-voxel-spacing	error	Non-positive voxel spacing pixdim=(<dx>, <dy>, <dz>) mm (all spatial spacings must be > 0).
M9503	nifti-singular-affine-transform	error	4x4 sform affine transformation matrix is singular or degenerate with det(A) = '<detA>'.
M9504	nifti-invalid-quaternion-norm	error	Invalid qform quaternion parameters (<b>, <c>, <d>): b^2 + c^2 + d^2 = '<normSq>' exceeds 1.0.
M9505	nifti-qform-sform-handedness-mismatch	error	Coordinate handedness mismatch between active qform (qfac sign '<qfacSign>') and sform (det sign '<sformDetSign>').
M9506	nifti-zero-intensity-scale-slope	error	Intensity scaling has scl_slope='<sclSlope>' with active scaling (scl_inter='<sclInter>'), zeroing all voxel intensities.
M9507	nifti-unsupported-datatype	error	Unsupported or invalid NIfTI/NRRD voxel datatype '<datatypeName>' (code='<datatypeCode>').
M9508	nifti-voxel-data-size-mismatch	error	Voxel payload count '<actualCount>' does not match expected '<expectedCount>' for dimensions <dimsDesc>.
M9509	nifti-empty-segmentation-mask	warning	Segmentation labelmap '<title>' contains zero foreground voxels across all anatomical labels.
M9510	nifti-anisotropic-slice-gap-warning	warning	Slice thickness dz='<dz>' mm exceeds in-plane resolution '<minInPlane>' mm by '<ratio>x' (> 5x threshold), risking severe 3D stair-step artifacts.

Generated from languages/nifti/src/lints/rules.ts. All languages →

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CLI Usage

# Inspect NIfTI/NRRD dimensions, voxel spacings, and RAS affine transforms
msx nifti inspect BrainAtlas.nii

# Validate qform/sform affine non-singularity and handedness consistency
msx nifti validate BrainAtlas.nii

# Extract 3D iso-surface mesh and ROI volumes from segmentation volume
msx nifti mesh BrainAtlas.nii

# Export reconstructed anatomical geometry to ISO 10303-21 STEP or OpenSCAD
msx nifti to-step BrainAtlas.nii > BrainAtlas.stp
msx nifti to-scad BrainAtlas.nii > BrainAtlas.scad