mahausmani/sa-inr

An arbitrary-scale SR method for reducing MR slice spacing.

This repository contains the official implementation for SA-INR introduced in the following paper:

Spatial Attention-based Implicit Neural Representation for Arbitrary Reduction of MRI Slice Spacing

The project page with video is at https://jamesqfreeman.github.io/SA-INR/.

Environment

• Python 3.9.2
• Pytorch 1.10.0+cu113
• nibabel, SimpleITK, pandas, scikit-image

Quick Start

1. We provide a pre-trained model checkpoint/model.pth for reducing slice-spacing of knee MRI.

2. Use the following command for reducing slice-spacing of a single test case.

python single_test.py --add_res --gpu [GPU] --save_dir [set a dir to save your images] --model_path [model_path] --nii_path [set the path to your test case] --slice_spacing [set your desired slice spacing] 

We also provide a knee MRI test/knee.nii.gz for testing.

Reproducing Experiments

Data Preparation

• Split your data into training set and test set.

• Write the paths of data to [your_dataset_name].json as in the following example.

{'train': [case1.nii.gz, case2.nii.gz...], 'test': [case3.nii.gz, case4.nii.gz...]}

• Edit train_SA_INR.yaml , change data: clinical_knee.json to data: [your_dataset_name].json

Training

python train.py --add_res --gpu [GPU] --save_path [set a dir to save your checkpoints] --config [train_SA_INR.yaml]

In default, the local-aware spatial attention (LASA) is applied to each query coordinate. One can use --add_branch to learn a gating mask for conditionally applying LASA.

Testing

python test.py --add_res --gpu [GPU] --save_dir [set a dir to save your images] --model_path [model_path]  --slice_spacing [set your desired slice spacing]

In the same way, one can use --add_branch for conditionally applying LASA.

Authors:

Xin Wang[1], Sheng Wang[1], Honglin Xiong[2], Kai Xuan[1], Zixu Zhuang[1], Mengjun Liu[1], Zhenrong Shen[1], Xiangyu Zhao[1], Lichi Zhang[1], Qian Wang[2]

Institution:

[1] School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China

[2] School of Biomedical Engineering, ShanghaiTech University, Shanghai, China