processing
Folders and files
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Scripts for (pre)processing recordings. Overview of (pre)processing: - "preprocessing_explore_parrm": identify optimal PARRM settings - "preprocessing": perform preprocessing - "preprocessing_project_coords": project ECoG coordinates to brain surface - "processing_annotations": annotate artefacts in data - "processing_coh": compute ImCoh - "processing_fmri_maps": compute whole-brain fMRI maps of connectivity - "processing_granger_causality": compute TRGC - "processing_mic": compute MIC - "processing_power_ssd": compute SSD - "processing_power_standard": compute power - "compute_tde": compute time delays Files generally have 3 types: - "single": process single recording - "preset": process multiple recordings serially - "preset_hpc": process multiple recordings in parallel (e.g. with a high-performance cluster), with associated shell script files Files have some shared constants: - "FOLDERPATH_DATA": directory where the data is stored - "FOLDERPATH_PREPROCESSING": directory where the preprocessing settings are stored and where the preprocessed data will be stored (e.g. in "Project/ Preprocessing") - "FOLDERPATH_PROCESSING": directory where the processing settings are stored and where the processed data will be stored (e.g. in "Project/Processing") - "DATASET": name of the cohort - "PRESET": group of recordings to analyse (see "Project/Preprocessing/ Settings/Generic/Data File Presets/README.txt" for details) - "ANALYSIS": if a preprocessing file, type of preprocessing to perform (see "Project/Preprocessing/Settings/Generic/README.txt" for details), or if a processing file, type of processing to perform (see "Project/Processing/ Settings/Generic/README.txt" for details) - "SETTINGS": type of data to compare (e.g. OFF therapy vs. ON levodopa, OFF therapy vs. ON STN-DBS; see "Project/Preprocessing/Settings/Specific/ README.txt" for details) - "PREPROCESSING": type of preprocessing to use (see "Project/Preprocessing/ Settings/Generic/README.txt" for details) - "SUBJECT": subject ID - "SESSION": session name - "TASK": task name - "ACQUISITION": acquisition name - "RUN": run number Constants marked with "# var" can be changed for analysis of different data or different methods.