├── .gitignore ├── .gitmodules ├── .zenodo.json ├── LICENSE ├── Makefile ├── README.md ├── code ├── README.md └── ppmi_snf │ ├── __init__.py │ ├── defaults.py │ ├── directories.py │ ├── preprocess.py │ ├── structures.py │ └── utils.py ├── container ├── README.md ├── Singularity └── run.sh ├── data ├── README.md ├── derivative │ ├── antslct │ │ ├── qc_ct.csv │ │ └── qc_rm.csv │ └── parcellated │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-033_deterministic_corticalthickness.csv │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-033_deterministic_corticalthickness.npy │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-060_deterministic_corticalthickness.csv │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-060_deterministic_corticalthickness.npy │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-125_deterministic_corticalthickness.csv │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-125_deterministic_corticalthickness.npy │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-250_deterministic_corticalthickness.csv │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-250_deterministic_corticalthickness.npy │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-500_deterministic_corticalthickness.csv │ │ ├── atl-Cammoun2012_space-MNI152NLin2009aSym_res-500_deterministic_corticalthickness.npy │ │ ├── atl-Pauli2018_space-MNI152NLin2009cAsym_hemi-both_deterministic_subcorticalvolume.csv │ │ ├── atl-Pauli2018_space-MNI152NLin2009cAsym_hemi-both_deterministic_subcorticalvolume.npy │ │ └── pdica_atrophy.csv └── raw │ └── ppmi │ └── bids │ └── tesla.csv ├── environment.yml ├── figures ├── figure_1.svg ├── figure_2.svg ├── figure_3.svg ├── figure_4.svg └── figure_s1.svg ├── manuscript ├── .gitignore ├── README.md ├── figures │ ├── data_concatenation.pdf │ ├── diffusion_embedding.pdf │ ├── network_creation.pdf │ ├── patient_clusters.pdf │ └── pdhc_clustering.pdf ├── main.pdf ├── main.tex └── refs.bib ├── requirements.txt ├── scripts ├── 01_preprocess │ ├── 01_parcellate_antslct.py │ └── 02_get_pdica_zscore.py ├── 02_analysis │ ├── 01_prepare_snf_data.py │ └── 02_snf_gridsearch.py ├── 03_results │ ├── 01_concatenation_vs_snf.py │ ├── 02_pd_patient_biotypes.py │ ├── 03_mri_contributions.py │ ├── 04_diffusion_embedding.py │ ├── 05_supplementary_results.py │ └── analysis.py └── README.md ├── setup.cfg └── walkthrough ├── 00_setting_up.md ├── 01_accessing_data.md ├── 02_converting_to_BIDS.md ├── 03_antslct_pipeline.md ├── 04_snf_analyses.md ├── README.md └── images ├── ppmi_add_to_collection.png └── ppmi_advanced_search.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/netneurolab/markello_ppmisnf/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 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