manuscript-binns_cortex_stn_comm

Code for the manuscript Binns et al. (Pre-print). DOI: 10.1101/2024.04.14.586969.

The repository has the following structure:

• processing - location of scripts for (pre)processing of data (view README)
• analysis - location of scripts for analysis of processed data (i.e. generating subject- and group-level results; view README)
• plotting - location of scripts for plotting results (view README), with images stored in figures
• Project - location of settings files and results (view README)
• coherence - internal scripts for performing the analyses
• DEMO - location of simulated data and example scripts for performing the analyses (view README)

The scripts have several external dependencies (the exact versions should be followed to ensure reproducibility):

• for Python, these should be acquired using the environment.yml file with conda. This will not take more than a few minutes if the libmamba solver is used, e.g.:

  conda env create --file=environment.yml --solver=libmamba
  

• for MATLAB (R2022b), these must be acquired manually (this will not take more than a few minutes):
  • SPM12 r7771
  • Lead-DBS v2.6
  • WJN Toolbox (tsbinns) v1.0.0

Testing for all code has been performed with Windows 11 and the package versions specified above.

The scripts expect data to be in the BIDS format.

The data used in the study can be made available conditionally to data sharing agreements in accordance with data privacy statements signed by the patients within the legal framework of the General Data Protection Regulation of the European Union. For this, you should contact the corresponding author ([email protected]) or the Open Data Officer ([email protected]).