Sdc

SDC - Susceptibility Distortion Correction for EPI/DWI

Part of the micaflow processing pipeline for neuroimaging data.

This module corrects geometric distortions in echo-planar imaging (EPI) MR images caused by magnetic field inhomogeneities. It implements the HYSCO (HYperellastic Susceptibility artifact COrrection) algorithm that uses a pair of images acquired with opposite phase-encoding directions to estimate and correct these distortions. The algorithm estimates a displacement field along the phase-encoding direction (typically y-axis) that can be used to unwarp the distorted images.

Features:

• B0 field estimation using phase-encoding reversed image pairs

• GPU acceleration with PyTorch for faster processing when available

• Automatic initial alignment using ANTs affine registration

• Advanced optimization using Alternating Direction Method of Multipliers (ADMM)

• Outputs both corrected images and estimated displacement fields for further usage

• Temporary file management for clean processing pipeline

API Usage:

micaflow SDC

–input <path/to/forward_phase_encoded.nii.gz> –reverse-image <path/to/reverse_phase_encoded.nii.gz> –output <path/to/corrected_image.nii.gz> –output-warp <path/to/displacement_field.nii.gz>

Python Usage:

>>> from micaflow.scripts.SDC import run
>>> run(
...     data_image="forward_phase_encoded.nii.gz",
...     reverse_image="reverse_phase_encoded.nii.gz",
...     output_name="corrected_image.nii.gz",
...     output_warp="displacement_field.nii.gz"
... )

Command Line Usage

micaflow SDC [options]

Source Code

View the source code: GitHub Repository

Description

This script corrects geometric distortions in echo-planar imaging (EPI)

MR images caused by magnetic field inhomogeneities. It uses the HYSCO algorithm with a pair of images acquired with opposite phase-encoding directions.

Full Help

╔════════════════════════════════════════════════════════════════╗
║               SUSCEPTIBILITY DISTORTION CORRECTION             ║
╚════════════════════════════════════════════════════════════════╝

This script corrects geometric distortions in echo-planar imaging (EPI)
MR images caused by magnetic field inhomogeneities. It uses the HYSCO
algorithm with a pair of images acquired with opposite phase-encoding
directions.

────────────────────────── USAGE ──────────────────────────
  micaflow SDC [options]

─────────────────── REQUIRED ARGUMENTS ───────────────────
  --input         : Path to the main EPI image (.nii.gz)
  --reverse-image : Path to the reverse phase-encoded image (.nii.gz)
  --output        : Output path for the corrected image (.nii.gz)
  --output-warp   : Output path for the estimated warp field (.nii.gz)

──────────────────────── EXAMPLE USAGE ───────────────────────
  micaflow SDC \
    --input main_epi.nii.gz \
    --reverse-image reverse_epi.nii.gz \
    --output corrected_epi.nii.gz \
    --output-warp warp_field.nii.gz

────────────────────────── NOTES ─────────────────────────
- The algorithm extracts the first volume from 4D input images
- GPU acceleration is used if available (recommended)
- The correction estimates a displacement field along the y-axis
- This implementation uses the HYSCO (HYperellastic Susceptibility
  artifact COrrection) algorithm