synthDIR
This repository contains our Keras GAN model and corresponding script for creating synthetic DIR images (plus uncertainty maps) from input FLAIR and T1w images.
We expect the keras model "ms_gan_generator.h5" to be stored in the same folder as this script!
Usage:
generate_synthDIR.py /path/t1/t1.nii.gz /path/flair/flair.nii.gz
T1 and FLAIR must be co-registered [1][2], skull-stripped [3] and in MNI152 space (1mm isotropic resolution) [4]. See the example T1 and FLAIR for details.
This scripts outputs two files:
/path/t1/synthDIR.nii.gz
/path/t1/synthDIR_ucMap.nii.gz
[1] https://github.com/ANTsX/ANTs
[2] https://github.com/KCL-BMEIS/niftyreg
[3] https://github.com/MIC-DKFZ/HD-BET
[4] http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
