In the last article I introduced Extended Streamline Tractography (XST). In this article I will talk talk about the best practices and supporting softwares when applying XST to real MR data.
- Preprocess DWI images
- Generate seeding coordinates from ROI mask
- Running XST
- Embedd diffusivity metrics onto the tractography model
The following are required to run the supporting scripts:
git clone https://github.com/sinkpoint/pynrrd.git python setup.py install
git clone https://github.com/sinkpoint/neuro-scripts.git
Then make sure to add the neuro-script repo dir to the path in
.bashrc. If you are on OSX then add it to
Preprocess DWI images
Diffusion weighted image (DWI) preprocessing involves a number of steps, including motion and eddy-current corrections, possibly reverse-phase encoding corrections, resampling ...more ...