oliverchampion

IVIMNET

This repository contains the code regarding our publication: Improved unsupervised physics-informed deep learning for intravoxel-incoherent motion modeling and evaluation in pancreatic cancer patients

PCA_denoising

The PCA denoising matlab algorithm used in the publication "Principal component analysis for fast and model-free denoising of multi b-value diffusion-weighted MR images" by Oliver J Gurney-Champion et al. in physics in medicine and biology in 2019.

DCENET

Neural networks for fitting DCE data

IVIM_tools

Matlab tools for intravoxel incoherent motion (IVIM) data, including kurtosis, stretched exponential, tri-exponential, mono-exponential and segmented fits in Matlab

Elastix_Matlab_wapper

A very quick and dirty simple wrapper for Elastix. Still requires a elastix installation. Also requires you to define the fitting parameters yourself in a text file. Handy in post processing scripts.

Advanced_MRI_lecture_4_qMRI

Exercises for the advanced MRI course, lecture 4 on quantitative MRI

AI_for_medical_imaging_course

This GIT contains the exercises and examples from the UvA/VU AI for medical imaging course.

BScThesis-AutoLiverSeg

Bachelor Thesis: Automatic Liver Segmentation of Quantitative MRI Data using U-Net and SegNet

DISPENSE

Stack of Spiral Aided Diffusion

hiddenlayer

Neural network graphs and training metrics for PyTorch, Tensorflow, and Keras.

MR_XCAT_qMRI

MRI_stuff

some Matlab code to analyse MRI

Nifti_and_Dicom

Some tools I use to read and write NIFTI and Dicom files.