Directory Structure

This repo expects a particular directory structure. Here is a brief description:

• PRJ_DIR: This is the folder containing the project. You will need to set it correctly for your environment in the utils.basics.py file.

• <PRJ_DIR>/Notebooks: all notebooks and scripts needed to re-create all figures in the manuscript.

• <PRJ_DIR>/Notebooks/utils: a series of functions and definitions used across several notebooks.

• <PRJ_DIR>/Data: this folder contains the representative time-series per ROI for the Craddock Atlas. These files were generated using notebook N00_Preparations.ipynb and a local copy of the data used in the original PNAS2015 work describing this dataset. You don't need to re-run this notebook, but to start on the next one.

• <PRJ_DIR>/Data_Interim: this folder will contain intermediate results such as sliding window correlation matrices, embeddings generated with the different methods, files with silhouette indexes, etc... Folders in this location will be populated by the different notebooks as analyses proceed.

• <PRJ_DIR>/Dashboard: this folder will contain a series of pre-generated figures and panda dataframes that allows the Embedding GUI to run more efficiently than if we were to regenerate those with every user interaction.

• <PRJ_DIR>/Logs.<<username>>: this code relies on swarm jobs to parallelize analyses. This is the folder where swarm jobs will save logs associated with job execution.

• <PRJ_DIR>/Swarm.<<username>>: This is the folder where notebooks will save swarm files to be submitted as batch jobs in the cluster.

• <PRJ_DIR>/Resources: Files with information about tasks, rois, etc:

  • PNAS2015_WinNames_wl45s_ws1p5s.txt: task associated with each sliding window (WL=25s | Ws = 1.5s)

  • ROI_Coordinates.txt: coordinates of all ROIs. We use this to know in which hemisphere they are.

• <PRJ_DIR>/Outputs/: Code will write intermediary files and figures to this folder.