figure_notebooks.md

Notebooks to recreate figures

Prerequisite

To run the notebooks make sure you are using the meld_environment and you have also installed these additionals packages :

• umap-learn

pip install umap-learn

Figure 1

Overview figure, composite of:

• Native subject meshes plot_one_subject_native.ipynb
• ComBat images age_curves.ipynb
• Left right asymmetry diagram asymmetry_synth.ipynb
• Cohorts from demographics_tables.ipynb
• Predictions from plotting_subjects_figure_8.ipynb
• UMAP from umaps.ipynb

Figure 2

Combat normalisation:

• age_curves.ipynb

Figure 3

Features as a function of geodesic distance from the lesion

• Analyse_features_distance.ipynb

Figure 4

UMAPs of manually-delineated lesion masks

• umaps.ipynb

Figure 5

Classifier predictions for individual subjects

• plotting_subjects_figure_3.ipynb

Figure 6

Logistic regression analyses

• read_results.ipynb

Figure 7

UMAPs of predicted lesions

• umaps.ipynb

Figure 8

Single subject saliency and MRIs

• plotting_subjects_figure_8.ipynb

Table 1

Demographics tables

• demographics_tables.ipynb

Table 2

Results tables

• read_results.ipynb

Table 3

Subgroup results tables

• read_results.ipynb