Simultaneous PET/MR scanners combine the high sensitivity of MR imaging with the functional imaging of PET. However, attenuation correction of breast PET/MR imaging is technically challenging. The purpose of this study is to establish a robust attenuation correction algorithm for breast PET/MR images that relies on deep learning (DL) to recreate the missing portions of the patient’s anatomy (truncation completion), as well as to provide bone information for attenuation correction from only the PET data. Three DL models, U-Net with mean absolute error loss (DL_MAE) model, U-Net with mean squared error loss (DL_MSE) model, and U-Net with perceptual loss (DL_Perceptual) model, were trained to predict synthetic CT images (sCT) for PET attenuation correction (AC) given non-attenuation corrected (NAC) PET (PET/MR) images as inputs. The DL and Dixon-based sCT reconstructed PET images were compared against those reconstructed from CT images by calculating the percent error of the standardized uptake value (SUV) and conducting Wilcoxon signed rank statistical tests.
Clone this repo:
git clone https://github.com/xli2245/Synthetic-CT-generation-from-NAC-PETMR
This project is implemented using Keras.
- create a conda environment
conda create -n tf2 python=3.7
conda activate tf2
- install necessary packages
conda install -c anaconda keras-gpu=2.3.1
conda install -c anaconda tensorflow-gpu=1.14.0
conda install -c conda-forge nibabel
conda install -c conda-forge matplotlib=3.4.3
conda install -c anaconda scikit-learn
conda install -c anaconda scikit-image
VGG 16 is used for perceptual loss calculation. In the first round, the VGG model was trained to discriminate the NAC PET and CT images
python ./discriminator/discriminator_PET.py
In the second round, it was trained to discriminate the sCT and CT images for better image feature caption.
python ./discriminator/discriminator_sCT.py
- Model training
python ./generator/main.py
- Model prediction
python ./generator/predict.py
