niftyregw 0.2.0

Thin wrapper of NiftyReg with Python and CLI interfaces.

niftyregw

Pythonic wrapper for NiftyReg, providing a modern CLI and Python API for medical image registration.

NiftyReg is a suite of tools for efficient medical image registration, developed at King's College London.

Installation

pip install niftyregw

Or with uv:

uv pip install niftyregw

CLI

niftyregw --help

Affine registration

niftyregw aladin \
  --reference ref.nii.gz \
  --floating flo.nii.gz \
  --output-affine affine.txt \
  --output-result result.nii.gz

Non-rigid registration

niftyregw f3d \
  --reference ref.nii.gz \
  --floating flo.nii.gz \
  --input-affine affine.txt \
  --output-cpp cpp.nii.gz \
  --output-result result.nii.gz

All subcommands

Subcommand	Description
install	Download and install NiftyReg binaries
aladin	Block-matching global (affine/rigid) registration
f3d	Fast Free-Form Deformation non-rigid registration
measure	Compute similarity measures between images
jacobian	Compute Jacobian-based maps from transformations
resample	Resample an image with a given transformation
tools	Image manipulation tools
average	Average images or transformations
transform	Manipulate and compose transformations

Python

from niftyregw import reg_aladin

reg_aladin(
    reference="ref.nii.gz",
    floating="flo.nii.gz",
    output_affine="affine.txt",
    output_result="result.nii.gz",
    rigid_only=True,
)

For any binary, use the generic run function:

from niftyregw import run

run("reg_f3d", "-ref", "ref.nii.gz", "-flo", "flo.nii.gz")