parent41/x-separation-uk_biobank

Changes to chisep for UKB scripts

x-separation application to UK biobank dataset

This repository contains the X-separation application for UK biobank datasets.

UKB dataset

The whole data of UK biobank can be accessed by https://www.ukbiobank.ac.uk/

Pretrained models

The checkpoints can be download form google drive link in /python/r2_r2star_mapping/checkpoints/download.txt

Requirements

MATLAB: R2021b
PYTHON: use env.yml file in python/r2_r2star_mapping
FSL built with wsl

x-separation reconstruction

• change 'path' in Biobank_x_sep_step0_Dicomprocessing.m, Biobank_x_sep_step1_GREprocessing.m, Biobank_x_sep_step2_DLpreprocessing.m, and Biobank_x_sep_step3_reconstrction.m
• run Biobank_x_sep_step0_Dicomprocessing.m, Biobank_x_sep_step1_GREprocessing.m and Biobank_x_sep_step2_DLpreprocessing.m
• move Data_to_gpu_t2map.mat and Data_to_gpu_t2starmap.mat to python\r2_r2star_mapping\data
• run predict_r2.py and predict_r2star.py
• move inference file to 'inf_from_gpu' which is made in your directory
• run Biobank_x_sep_step3_reconstrction.m