xQSM

Yang Gao, Xuanyu Zhu, Bradford A. Moffat, Rebecca Glarin, Alan H. Wilman, G. Bruce Pike, Stuart Crozier, Feng Liu, Hongfu Sun, 2020. xQSM: quantitative susceptibility mapping with octave convolutional and noise-regularized neural networks.

Setup xQSM for SEPIA

  1. Download deepMRI from GitHub
  2. Download the pre-trained xQSM here as mentioned in the instruction on GitHub
  3. Specify the full path to deepMRI code as ‘deepMRI_HOME’ in setup_xQSM_environment.m in SEPIA_HOME/addons/qsm/xQSM/
  4. Specify the full path to the folder containing the pre-trained networks (should be checkpoints/) from (2) as ‘checkpoints_dir’ in setup_xQSM_environment.m

Your setup_xQSM_environment.m should look something like this:

../../_images/xQSM_setup.png

Warning

The support this method is still in an early stage and only tested on a Linux machine.

xQSM panel

In the xQSM panel you can select one of the five provided pre-trained networks.

../../_images/xQSM.png