04_snf_analyses.md

Reproducing the analyses

Now that everything is installed and downloaded and pre-processed, you likely want to run the analyses! Assuming we set everything up correctly (fingers crossed), the following command, run from the root of the repository, should do the trick:

make all

You'll get a whole lot of outputs and numbers printed to the screen, most of which should match those we report in the associated manuscript. (If something seems amiss, please let us know!)

Below, we'll describe what each script that the above commands runs is doing in a bit more detail.

Preparing for SNF

The SNF procedure

Data concatenation versus SNF

PD patient biotypes

MRI contributions

Diffusion embedding

Supplementary analyses