neuropixels_preprocess/example_extract_postcuration_params.txt at main · vandermeerlab/neuropixels_preprocess · GitHub

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# Extract Units Parameters File
# This file configures the behavior of extract_units_post_curation.py for extracting sorted units after Phy curation

# Required Parameters
# Path to the CatGT output directory with tcat raw recordings
CATGT_OUTPUT_DIR=E:\STNPilot\Test\catgt_M511-2024-11-14_g0

# Path to save output MAT files with extracted units
OUTPUT_DIR=E:\STNPilot\Test\preprocessed

# Session identifier used for logging and file naming
SESSION_ID=M511-2024-11-14

# Processing Options
# List of probes to process (comma-separated)
PROBE_INDICES=0,1

# Probes that were sorted per-shank (comma-separated; must match PROCESS_BY_SHANK_FOR used in
# extract_lfp_and_run_ks4.py). Probes listed here need "imec{p}_shank{s}" keys (e.g. "imec0_shank0")
# in SORTER_OUTPUT_FOLDERS/PREPROCESS_FOLDERS; every other probe uses "imec{p}" (e.g. "imec1").
# Units from all shanks are merged into one per-probe output file (unit_type_units_imec{p}.mat)
# so downstream NWB loading is unchanged. Empty = no probe by shank.
PROCESS_BY_SHANK_FOR=

# Shanks to process for each by-shank probe (comma-separated)
# SHANK_INDICES=0,1,2,3
# Optional per-probe override, when two by-shank probes have different shank sets:
# SHANK_INDICES_IMEC0=0,1

# Sorter output folders (JSON format)
# Per-probe keys (probes not in PROCESS_BY_SHANK_FOR):
SORTER_OUTPUT_FOLDERS={"imec0": "F:\\KS4_outputs\\M511-2024-11-14_imec0\\sorter_output", "imec1": "F:\\KS4_outputs\\M511-2024-11-14_imec1\\sorter_output"}
# Per-shank keys (probes in PROCESS_BY_SHANK_FOR):
# SORTER_OUTPUT_FOLDERS={"imec0_shank0": "F:\\KS4_outputs\\SESSION_imec0_shank0\\sorter_output", "imec0_shank1": "F:\\KS4_outputs\\SESSION_imec0_shank1\\sorter_output", "imec0_shank2": "F:\\KS4_outputs\\SESSION_imec0_shank2\\sorter_output", "imec0_shank3": "F:\\KS4_outputs\\SESSION_imec0_shank3\\sorter_output"}
# Both key styles may be mixed in one dict, e.g. PROCESS_BY_SHANK_FOR=0 with probes 0 and 1:
# SORTER_OUTPUT_FOLDERS={"imec0_shank0": "...", "imec0_shank1": "...", "imec0_shank2": "...", "imec0_shank3": "...", "imec1": "..."}

# SI preprocess folders containing binary recordings (JSON format, same key style as above)
# Per-probe keys:
PREPROCESS_FOLDERS={"imec0": "E:\\STNPilot\\Test\\preprocessed\\imec0_si_preprocess", "imec1": "E:\\STNPilot\\Test\\preprocessed\\imec1_si_preprocess"}
# Per-shank keys:
# PREPROCESS_FOLDERS={"imec0_shank0": "F:\\KS4_outputs\\SESSION_imec0_shank0_si_preprocess", "imec0_shank1": "F:\\KS4_outputs\\SESSION_imec0_shank1_si_preprocess", "imec0_shank2": "F:\\KS4_outputs\\SESSION_imec0_shank2_si_preprocess", "imec0_shank3": "F:\\KS4_outputs\\SESSION_imec0_shank3_si_preprocess"}

# Whether to extract and save unit waveforms
SAVE_WAVEFORMS=true

# Unit types to extract
EXTRACT_GOOD_UNITS=True
EXTRACT_MUA_UNITS=True

# Number of parallel jobs for waveform extraction (-1 uses the maximum possible channels)
NUM_JOBS=-1