nii — command-line interface

nii <command> PATH OUTPUT_DIR [options]

For rotate, flip, crop-content, and rescale, PATH may be a single NIfTI file or a folder (auto-detected; a folder is processed as a dataset). crop takes a single file; from-dicom takes a DICOM series folder. Each command prints the output path(s) it wrote. Exit code 0 on success, 2 on a usage / runtime error.

Commands

Command	Purpose	Key options
rotate	Rotate by k×90° in a voxel plane (lossless)	--k INT (default 1), --axes A B (default 0 1)
flip	Mirror along a voxel axis	--axis {0,1,2} (default 0)
crop	Crop to an explicit voxel box	--bbox X0 X1 Y0 Y1 Z0 Z1 (required)
crop-content	Crop to the minimal foreground box	--threshold FLOAT, --margin INT
rescale	Linearly rescale intensities	--out-min, --out-max, --in-min, --in-max
to-dicom	Convert NIfTI → DICOM series	--series-description STR
from-dicom	Convert DICOM series folder → NIfTI	—
preview	Render a slice-montage PNG of a volume	--view {axial,coronal,sagittal}, --num-slices INT, --cols INT

Examples

# Rotate 90° in the axial plane, save into out/
nii rotate scan.nii.gz out/ --k 1 --axes 0 1

# Mirror every volume in a folder along the first axis
nii flip scans/ out/ --axis 0

# Crop to an explicit voxel box
nii crop scan.nii.gz out/ --bbox 10 100 10 100 5 60

# Trim empty borders, keeping a 2-voxel margin
nii crop-content scan.nii.gz out/ --margin 2

# Rescale intensities to 0–255 (e.g. for 8-bit export)
nii rescale scan.nii.gz out/ --out-min 0 --out-max 255

# Convert to a DICOM series and back
nii to-dicom scan.nii.gz out/
nii from-dicom dicom/case_01/ out/

# Render a montage PNG to eyeball a result
nii preview out/scan_content.nii.gz out/ --view axial --num-slices 16

Output filenames carry an operation suffix: _rot<k>, _flip<axis>, _cropped, _content, _rescaled. to-dicom writes a folder named after the input volume containing one .dcm per slice.