A Deep learning method for Diffusion MRI Segmentation (DDSeg)
This code implements deep learning tissue segmentation method using diffusion MRI data, as described in the following paper:
Fan Zhang, Anna Breger, Kang Ik Kevin Cho, Lipeng Ning, Carl-Fredrik Westin, Lauren O'Donnell, and Ofer Pasternak.
Deep Learning Based Segmentation of Brain Tissue from Diffusion MRI
NeuroImage 2021.
Please download the pre-trained CNN models and testing data:
https://github.com/zhangfanmark/DeepDWITissueSegmentation/releases
Download Unet-DTI-n5-ATloss-GMWMCSF.zip and Unet-MKCurve-n10-ATloss-GMWMCSF.zip, and uncompress them to the CNN-models folder.
Download test_sub_CAP.zip and test_sub_HCP.zip, and uncompress them to the test folder.
The code allows tissue segmentation using DTI parameters (single shell dMRI data) and using MKCurve (multi shell dMRI data with MKCurve corrected data). See scripts under the test folder for examples.