openrecon-ants

MR Host screenshot from a Siemens 7T Terra.X in XA60A.
Sequence Non-selective 3D SPACE.
From left to right Original, brain mask (SynthStrip), N4BiasFieldCorrection (ANTs) in brain mask, DenoiseImage (ANTs) in brain mask after N4BiasFieldCorrection.
From top to bottom 3D FLAIR with Circular Polarization (CP), 3D FLAIR with Universal Pulses (UP), 3D DIR with UP.

ANTs using ANTsPy in OpenRecon.
Brain masking is performed by SynthStrip

Based on https://github.com/benoitberanger/openrecon-template

Features

This OR performs ANTs image operations :

• N4BiasFieldCorrection
• DenoiseImage
• N4BiasFieldCorrection then DenoiseImage (default)
• DenoiseImage then N4BiasFieldCorrection

There is an option, a checkbox, to save original images and intermediate images. (default is True)

There is an option, a checkbox, to apply in brainmask using SynthStrip. (default is True)

Build

Requirements for building :

• python 3.12
• jsonschema

Python environment manager is strongly recomanded :

conda create --name openrecon-ants
conda install python=3.12
pip install jsonschema

Build with :

python build.py

Offline test and dev

Python modules :

• ismrmrd
• pydicom
• pynetdicom
• antspyx
• torch
• surfa

pip install ismrmrd pydicom pynetdicom antspyx torch surfa

Follow guidelines in https://github.com/benoitberanger/openrecon-template

TODO

Add fields in the UI to tune N4BiasFieldCorrection and DenoiseImage