Repository for studying correlations between neuraldegeneration volume over time in patients with mild Alzheimer's vs. severe. The published paper can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10406695/
dataset: first agree to the user agreement by Alzheimer's Disease Neuroimaging Initiative: ADNI and download the ADNI1 3Y1.5T Longitudinal FreeSurfer dataset by University of California, San Francisco from the website. Make sure the files UCSFFSL_02_01_16.csv, UCSFFSL_DICT_11_01_13.csv and the subject CDR ratings in CDR.csv are in a directory named dataset in the working directory with the notebooks.
preprocess: notebook on preprocessing data dataset. If input data has the same format as our example, can also preprocess into input format
pipeline_functions: joint graph embedding algorithm and f-type statistics analysis functions with and without confounder regression, and helper functions
joint_graph_embedding_analysis: notebook on running the algorithm and analysis
requirements.txt: requirement packages and versions
For running on the example dataset, first run preprocess notebook, then run joint_graph_embedding_analysis.
documentation generated with sphinx software (https://www.sphinx-doc.org/en/master/), code documentation can be found in docs/build/html/index.html