Coregister

coregister - Image Registration for Aligning Neuroimaging Data

Part of the micaflow processing pipeline for neuroimaging data.

This module performs comprehensive image registration between two images using the Advanced Normalization Tools (ANTs) SyNRA algorithm, which combines rigid, affine, and symmetric normalization transformations. It aligns a moving image with a fixed reference space, enabling spatial normalization of neuroimaging data for group analysis, multimodal integration, or atlas-based analyses.

Features:

Combined rigid, affine, and SyN nonlinear registration in one step
Bidirectional transformation capability (forward and inverse)
Option to save all transformation components for later application
Uses ANTs’ powerful SyNRA algorithm for optimal accuracy
Preserves header information in the registered output images

API Usage:

micaflow coregister: –fixed-file <path/to/reference.nii.gz> –moving-file <path/to/source.nii.gz> –output <path/to/registered.nii.gz> [–warp-file <path/to/warp.nii.gz>] [–affine-file <path/to/affine.mat>] [–rev-warp-file <path/to/reverse_warp.nii.gz>] [–rev-affine-file <path/to/reverse_affine.mat>]

Python Usage:

>>> from micaflow.scripts.coregister import ants_linear_nonlinear_registration
>>> ants_linear_nonlinear_registration(
...     fixed_file="mni152.nii.gz",
...     moving_file="subject_t1w.nii.gz",
...     out_file="registered_t1w.nii.gz",
...     warp_file="warp.nii.gz",
...     affine_file="affine.mat",
...     rev_warp_file="reverse_warp.nii.gz",
...     rev_affine_file="reverse_affine.mat"
... )

Command Line Usage

micaflow coregister [options]

Source Code

View the source code: GitHub Repository

Description

This script performs linear (rigid + affine) and nonlinear (SyN) registration: between two images using ANTs. The registration aligns the moving image to match the fixed reference image space.

Full Help

╔════════════════════════════════════════════════════════════════╗
║                      IMAGE COREGISTRATION                      ║
╚════════════════════════════════════════════════════════════════╝

This script performs linear (rigid + affine) and nonlinear (SyN) registration
between two images using ANTs. The registration aligns the moving image to
match the fixed reference image space.

────────────────────────── USAGE ──────────────────────────
  micaflow coregister [options]

─────────────────── REQUIRED ARGUMENTS ───────────────────
  --fixed-file   : Path to the fixed/reference image (.nii.gz)
  --moving-file  : Path to the moving image to be registered (.nii.gz)
  --output       : Output path for the registered image (.nii.gz)

─────────────────── OPTIONAL ARGUMENTS ───────────────────
  --warp-file      : Path to save the forward warp field (.nii.gz)
  --affine-file    : Path to save the forward affine transform (.mat)
  --rev-warp-file  : Path to save the reverse warp field (.nii.gz)
  --rev-affine-file: Path to save the reverse affine transform (.mat)

────────────────── EXAMPLE USAGE ────────────────────────

# Register a moving image to a fixed image
micaflow coregister --fixed-file mni152.nii.gz --moving-file subject_t1w.nii.gz \
  --output registered_t1w.nii.gz --warp-file warp.nii.gz --affine-file affine.mat

────────────────────────── NOTES ───────────────────────
• The registration performs SyNRA transformation (rigid+affine+SyN)
• Forward transforms convert from moving space to fixed space
• Reverse transforms convert from fixed space to moving space
• The transforms can be applied to other images using apply_warp