Phase 1: BIDS import and preprocessing pipeline (R3-mini)

[MinaNourhashemi]

Closes #11. Part of #10.

Summary

• Implements the Phase 1 HBN ERSP preprocessing pipeline targeting R3-mini (100 Hz, 20 subjects)
• One MATLAB function per step; all callable from the command line via run_phase1('r3mini')
• Full R3 blocked until this pipeline validates end-to-end on mini

Files

File	Purpose
config/cfg_r3mini.m	R3-mini paths and preprocessing parameters
phase1/p1_import_bids.m	pop_importbids wrapper; outputs raw ALLEEG
phase1/p1_highpass.m	1 Hz FIR highpass via pop_eegfiltnew
phase1/p1_cleanline.m	CleanLine at 60/120/180 Hz
phase1/p1_channel_reject.m	clean_rawdata channel rejection only (ASR off)
phase1/run_phase1.m	Master script; saves sets + phase1_report.mat

Deviations from reference pipeline (study_handy_scripts.m)

• ASR disabled: BurstCriterion = 'off' and WindowCriterion = 'off'. The reference uses ASR defaults; this pipeline skips it because ASR modifies the continuous signal in ways that bias ICA decomposition (Phase 2). Channel-level rejection only.
• Checkpoint save after import: raw sets written to derivatives/raw/ before filtering to allow recovery without re-running BIDS import.

Acceptance criteria status

• All 6 files implemented with explicit parameter justification comments
• run_phase1('r3mini') runs without error (blocked: R3-mini data not yet downloaded; validated by code review only)
• Channel retention logged per subject; warn if <90%
• derivatives/ in .gitignore (data never committed)
• Deviations from reference pipeline documented above and in phase1/README.md

Test plan

• Download R3-mini (20 subjects from s3://fcp-indi/data/Projects/HBN/BIDS_EEG/cmi_bids_R3)
• Run matlab -nodisplay -nosplash -r "addpath(genpath('sessions/week-03/practicum')); run_phase1('r3mini'); exit"
• Confirm all subjects produce *_preproc.set in derivatives/preproc/
• Confirm all subjects retain >90% channels (128-channel HydroCel net)
• Confirm phase1_report.mat saved with per-subject counts