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Fix/bids conversion fixes#1049

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bruAristimunha merged 19 commits intodevelopfrom
fix/bids-conversion-fixes
Mar 30, 2026
Merged

Fix/bids conversion fixes#1049
bruAristimunha merged 19 commits intodevelopfrom
fix/bids-conversion-fixes

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bruAristimunha and others added 12 commits March 26, 2026 10:28
- bids_interface: crop signal to exact data records for BDF/EDF export
  (handles both integer and non-integer sampling rates), add standard
  montage fiducials when missing from head coordinate frame
- bnci_2016_002: fix KeyError in event_mapping for marker_labels
- bnci_2022_001: handle lowercase 'trigger' attribute in .mat files
- kaneshiro2015: detect truncated downloads via HTTP range request and
  re-download automatically (Stanford server uses chunked transfer)
- lee2024: add annotations from stim channel events for BIDS compat,
  fallback to dummy annotation when stim channel is empty
- martinezcagigal2023_checker/pary: convert data from uV to V before
  creating RawArray (fixes BDF physical_range overflow)
- triana_guzman2024: gracefully skip subjects with corrupt .set files
- zuo2025: handle 'data' key in addition to 'EEG' in .mat files
- chang2025: gracefully skip subjects with missing directories or
  .set files instead of crashing (subject S211 has no data upstream)
- guttmann_flury2025: fix channel types (Trig->stim, HEO/VEO->eog,
  M1/M2->misc) to prevent BDF export OSError from trigger channel
  values exceeding EEG physical range limits
Force datasets to include all runs/conditions that are excluded by
default for benchmarking convenience: Lee2019 test runs, Speier2017
online runs, RomaniBF2025ERP inference/failed sessions, Sosulski2019
SOA 60ms. Also add BDF to _FORMAT_EXTENSION_MAP.
- Expose motor_imagery and mental_arithmetic as keyword-only parameters
  on Shin2017A (default: MI=True, MA=False) and Shin2017B (default:
  MI=False, MA=True), preserving backward compatibility
- Update conversion script to re-instantiate Shin2017A/B with both
  conditions enabled for complete NEMAR deposits
- Lee2019: add 'rest' annotation to resting state runs so BIDS export
  doesn't fail with missing annotations error
- bids_interface: add BDF to _FORMAT_EXTENSION_MAP (was only local edit)
- bbci_eeg_fnirs: Shin2017A/B motor_imagery/mental_arithmetic params
  (already in previous commit, ensuring consistency)
- Add 'rest' annotation for BIDS export compatibility
- Include EMG channels in resting state runs when available,
  matching the main run data structure
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@bruAristimunha bruAristimunha merged commit e0c6dc6 into develop Mar 30, 2026
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@bruAristimunha bruAristimunha deleted the fix/bids-conversion-fixes branch March 30, 2026 08:59
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